Why did the Manties not embrace a deep-penetration strategy immediately?
Simple answer: their war-fighting doctrine was out of date, although there were some additional problems which had nothing to do with whether or not their strategic thinking was outdated.
It may surprise some of you to learn this, but despite Hamish Alexander and quite a few other very brainy folks on the Manticoran side, Nobody had fought a war on this scale -- either in terms of the size of the fleets involved, or in terms of the spatial distances involved -- in centuries, if ever. Everyone involved was sailing into terra incognita, and nobody on either side was prepared to embrace a high-risk, unproven strategic approach as long as they weren't in danger of being pounded under in the short term. So, since traditional strategic wisdom emphasized the necessity of securing the flanks and rear (and logistics corridors) of your fleet as you advanced, the major war fighting fleets adopted a policy of relatively short-legged offensives on a star-by-star basis.
This decision was also influenced by the fact that, as I've pointed out many times before, both sides had to keep very strong forces tied down to protect their central nodes against some sort of deep-penetration attack by the other side. This was especially true for Manticore, since if the Manticoran home system was lost or its infrastructure was crippled, the war was over, no matter what else happened. Even if Nouveau Paris and the Haven System were completely wrecked, the industrial capacity of the People's Republic, while hurt, would still have been substantially intact. Thus, the prize for taking out Haven (or any other major Havenite industrial node) would have been relatively much smaller for Manticore than the reverse would have been for the Peeps, and Manticore was not prepared to risk uncovering its strategic center in order to launch an attack which probably wouldn't be decisive even if it succeeded. This limited the sizes of the fleets available for offensive action, which was another reason that they went for relatively short-ranged campaigns on a star-by-star basis.
I've already commented in other places on the fact that the fundamental prewar and early-war strategies involved were attritional, not formulated in terms of maneuver and taking out targets far behind the front lines. This, again is a reason for short-ranged offensives which allow you to operate relatively cautiously while still inflicting losses on the other side. About the only exception to the star-by-star approach on the part of the Star Kingdom was the massive effort involved in finally taking Trevor's Star away from the People's Republic, and that was a strategic necessity for two reasons. First, it relieved a direct threat to the Manticoran home system -- one which had occupied a great deal of prewar thought, worry, and planning on Manticore's part. Secondly, it tremendously relieved the pressure on Manticoran logistics for operations deeper into the People's Republic's strategic glacis and, eventually, into the territory of the People's Republic itself. This was specifically referenced in the books, I believe. In addition, however, by taking Trevor's Star, the Manties found themselves in the rear -- in force -- of many of the Peeps' forward bases, which (under the traditional thinking which still dominated both navies at that point) essentially led the Peep admiralty to pull back steadily from their prewar high-water mark.
There's another reason for much of the unwillingness to hit vital targets deep behind the frontier. If you look at the majority of the battles fought early in the war, especially the ones in which the Manties were the aggressors, they were being fought over star systems outside the national boundaries (and primary defensive perimeters) of either side. There was a very good reason for that. Even with the early-generation missile pods, tangling with the fixed defenses of a major star system was not a cost-effective proposition. If taking the system out would be strategically decisive in determining the course of the war, that was one thing. If, however, such an attack represented only one step in an ongoing strategy -- that is, if the operation would have to be repeated, possibly several times -- it was a nonstarter. In effect, going after fortified systems -- even the sort of second-tier systems Honor and Eighth Fleet were attacking in At All Costs -- the prewar missile defenses were so heavy that the Manticoran qualitative advantage would have been considerably more than offset. If the Manties could have pursued such a strategy with the assurance that they would be destroying an amount of mobile combat power at least proportionally equivalent to what they were losing, they might have embraced it anyway, since they'd really gained pretty much parity in wallers at a fairly early stage in the war. However, what they would have been losing was their mobile combat power while the Peeps would have been losing fixed combat power which couldn't have been brought to bear in a mobile war, anyway. The Peeps would have loved that particular Manticoran strategy.
(By the way, much of what I've discussed above no longer applied by the time we get to Operation Cutworm. The missile defenses which were such a threat in pre-MDM days were the product of literally decades of investment and emplacement by both sides. With the advent of the MDM pod, and the tremendous increases in the throw weight of wallers, both sides had been forced to concentrate their available resources on building additional mobile platforms, which could be used both offensively and defensively. As a consequence, the fixed defenses of most star systems had not been upgraded significantly. Remember that there is discussion on the Havenite side after Honor's first raids about the fact that "the new missile pods" haven't arrived yet in several star systems. This is because providing the fixed defenses had such a much lower priority than building new warships.)
Once the missile pod came along, the strategic environment began to change, given the quantities of firepower -- long-range firepower -- which mobile forces could now project. However, until Manticore fielded the MDM, the sheer numbers involved still gave the defenses the decisive edge in attacks on strategically significant star systems. Once the MDM was available, it was possible for strategists like Hamish Alexander to project operations like Buttercup, and the era of deep-penetration strategy was born (or reborn, as the case may be).
Looking back from a post-Buttercup position, it is obvious to several of the strategic thinkers on either side that a deep-penetration strategy might, indeed, have been feasible even before the MDM, assuming that a sufficient number of wallers could have been concentrated, and that a sufficient number of pods could have been deployed. This is part of what Theisman was talking about when he commented to Eloise Pritchart that it had been proven that it was possible to fight a decisive, deep-strike war, after all. None of that, however, was evident to Manticore in the early stages of the first war. All of it grew out of changes in weaponry, the changes in tactics which those weaponry changes provoked, and the strategic and tactical experience (and confidence) which had been gained in the decade or so of fighting since the outbreak of the war at Hancock Station. And it might be pointed out that the strategist who actually first embraced the deep-strike approach wasn't Manticoran at all. It was Esther McQueen, who (in my opinion) was probably the only senior strategist in Haven's service who was superior to Thomas Theisman as a strategist. Her offsetting weaknesses in terms of personal ambition (and the baggage of hostility/distrust from Saint-Just and StateSec) were enough to cripple, or at least significantly limit, the impact that her strategic instincts had on the war, but even the single full-scale operation she was able to launch -- Operation Icarus -- had a major effect on the remaining course of the war. Not least because of the impact that it had on the thinking of people like Hamish Alexander when they found themselves possessed of weapons superior to anything she'd had.