Goals of Thunderbolt
I can see why the ships were a target but most good RMN officer's were not on them. And there is still home fleet plus the ships being built in Manticore. And then there is Elizabeth's hatred of Haven which had to have been known. But the big problem I have is that Thiesman seems too smart to think that he could use a military victory to force Manticore to the peace table.
First, Theisman is SecWar and CNO, not President. He carries out the orders he's given or he resigns in protest; he wasn't the one who made the policy which led to the resumption of hostilities.
Second, why do you assume that "most of the good RMN officers" weren't on the ships? The majority of good flag officers (or at least a large percentage of them) might have been beached, but the experienced personnel (including officers) needed to actually crew and fight the ships (not to mention providing the next generation of flag officers) were still on them. Kill enough experienced captains, commanders, and lieutenants and you make an even bigger hole in your opponent's combat power than you do picking off Admiral Yammamoto over the SW Pacific. Nor are the ships themselves a target to be despised. Building times are in years; trash the existing fleet platforms and take our Grendlesbane, and you have bought a window of say three years in which the other side is going to be fully occupied replacing its lost inventory of wallers while you go right on adding to your own.
"Home Fleet and the ships being built in Manticore" would have been much, much weaker than the RMN with all the ships which were supposed to be destroyed in Thunderbolt, especially with the loss of Grendelsbane. The ships under construction in Manticore had been made the priority by the Janacek Admiralty when it finally twigged to the fact that the Republic actually had a modern fleet. As a consequence, there weren't that many ships under construction in the Home System when Haven pulled the trigger on Thunderbolt --- the High Ridge government hadn't been able to lay down a bunch more because it had already spent the "war budget" funds on other (largely corrupt) programs, and they'd already completed the ones which had been laid down by the Cromarty Government when they gave preference to the Home System over Grendelsbane on the theory that spreading the money and jobs around the Home System would be good politics.
Elizabeth's hatred of Haven was, of course, well known, if not all the personal reasons for it. So what? She'd just demonstrated she either couldn't get rid of High Ridge or else agreed with his policies (remember, this is the Republic looking at Manticore from the outside), which, in turn, demonstrated stupidity (unlikely) or a loss of ability to strongly enfluence policy on her part. That loss of ability would be subject to change, of course, but it did tend to suggest that her viewpoint alone was far from the only determinant in Manty foreign policy. Moreover, all the hatred in the world wasn't going to change the facts of a serious Manty military defeat, especially when the terms being offered would be reasonable.
I have to ask: how does a nation which has been soundly defeated avoid the peace table? Thunderbolt by itself was not intended to "force" Manticore to the peace table, though no one in Haven would have objected if it had had that effect. Thunderbolt was the first stage in a larger war strategy, and had that strategy worked --- had the RMN been defeated --- then Manticore would have had no more option about negotiating than Haven did when Honor arrived there with Eighth Fleet in MoH.