Harvest Joy's first transit of the Torch terminus
The ambush of Harvest Joy. First, Harvest Joy was a single converted, obsolescent cruiser, not a superdreadnought, not an attacking battle fleet, and not even anticipating the remote possibility of an attack. Why in the world should she have been expecting anything of the sort? And why shouldn't the people waiting to deal with anyone coming through the terminus have assumed that their ambush would come as a total surprise to any new arrivals?
Most wormhole termini are light-hours from any star. If you don't already know the thing is there, then you're not going to be picketing it. So, by process of elimination, if it's an unexplored terminus, no one is going to know where you're going to come out to ambush you in the first place. Ergo, sudden, unprovoked attack is not something anyone ever worries about in wormhole survey work in the Honorverse.
Now, I realize there was discussion about whether or not Mesa had already explored the terminus. The conclusion, if you recall, was basically "We can't know for sure, because we didn't find any correspondence saying that they had explored it." What that really equated to in the minds of most of the people involved was "They probably never did explore it, because not only did we never find any correspondence, but they never used or exploited it." Don't forget, at this point despite all of the distrust of Manpower and Mesa generally, despite any clues which might be starting to percolate through, nobody on Torch knows about the Alignment or has any reason to expect those greedy, nasty people on Mesa to have denied themselves the economic benefits of using a wormhole connection if they knew where it went. All of this means the fundamental assumption of the people mounting the expedition was that Harvest Joy would emerge back into normal-space a long way away from any potential threat. The danger, such as it was and what there was of it, lay with making transit through an unexplored terminus which had that inexplicable spike associated with it, and that's what everyone's mind was on.
Now, in addition to assuming (quite justifiably) that nobody coming through from the other side would anticipate an immediate attack, the guys setting the ambush were perfectly well aware that the terminus was being surveyed and that only a single survey ship was involved. This was not an overnight process, if you'll recall. There was plenty of time for the Alignment to figure out that it wasn't going to be all that much longer before a survey ship came poking through from the Congo side. They knew they weren't going to be looking at a superdreadnought coming bursting through, all weapons manned, all sensors searching for hostiles. In fact, they had a pretty good idea of exactly which ship it was going to be. And they kept only two of their ships on rotating readiness, with their computers prepped to take the shot, to handle the anticipated intruder, so crew fatigue wasn't exactly going to be a crippling problem for them. And, I might point out, we have the perspective of none other than a Mannerheim System-Defense Force flag officer to tell us that the way they handled Harvest Joy was neither risky nor any sort of tactical necessity.
From the above, I think it should be fairly evident that this was a one-off situation. However, there seem to be some additional misconceptions floating around. Specifically, discussion as to whether or not the Trevor's Star terminus of the Manticoran Wormhole Junction was used during the period when Trevor's Star was held by the People's Republic. The answer is that, yes, it was. Don't forget that the Manticoran Wormhole Junction is something like two light-hours from Manticore-A. That's enough "strategic depth" for the Star Kingdom to feel relatively confident that even an invasion fleet which managed to take out all of the Junction's immediately adjacent infrastructure and fixed defenses could be intercepted by Home Fleet well short of the planets of Manticore or Sphinx. The reason I make this point is that I want it clearly understood that what we're talking about here is not a dagger pressed to the throat of the Star Kingdom, but rather more analogous to allowing neutral commercial traffic to pass through a vital international waterway (like the Arabian Gulf) in which one belligerent has a huge strategic interest. I'm obviously not saying that no precautions were taken, only that procedures could be worked out.
Remember that each terminus has its own separate arrival and departure lanes. (This has been referenced in the books.) That is, an inbound ship is not going to come remotely close to running into an outbound ship, so sequencing transits is most important - from a safety perspective - from the departure end, not the arrival end. Second, everyone on both sides knows exactly where any ship from the other side is going to arrive. Third, I never said there were no warships anywhere in close proximity to the emergence point; I said the forts were well back, outside energy range. Fourth, no one has ever said at any time that the Trevor's Star terminus served only Havenite commerce. In fact, if you look at what happened to Haven's right of transit following the events in On Basilisk Station, there wouldn't have been much point in my specifying that Havenite ships had been denied passage if other ships weren't continuing to enjoy passage.
So here's what happened, people. After open hostilities began, additional restrictions were placed on all passage through the Trevor's Star terminus of the Junction. Light warships were placed within energy range of the emergence point, and it was made clear to everyone involved that any ship coming through which did not immediately follow the procedures on which they had been thoroughly briefed before being allowed transit or failed to conform with any additional orders from traffic control after making transit, would be fired upon and destroyed. Stringent inspection procedures were put in place, which included stem-to-stern customs inspections, searches for weapons, documentation checks, etc. The precautions weren't perfect (by the nature of things there are no perfect precautions), but they were more than sufficient to deal with the potential threat which could be represented by any single merchant ship (or Q-ship) making transit, especially when the ship in question was two light-hours away from any of the Star Kingdom's inhabited planets. Those inspection procedures were also applied to ships departing through that terminus. Cargoes were subject to inspection, items which the Star Kingdom had declared contraband were subject to seizure, vessels suspected of intending to violate Manticore's restrictions on what could and could not pass through the terminus were subject to seizure,, etc. Traffic with diplomatic immunity or which belonged to one of the major service organizations was allowed to pass without inspection, but only aboard very small vessels which were under observation the entire time. The major defensive works, on the other hand - the forts - were far enough back to be out of range in the event of any insane mass transit, and to have enough space between them and the terminus (space equaling reaction time, in this case) to be able to take at least some time analyzing the threat before opening fire. But the entire time, there were light warships, inside the volume of the Junction itself, to do to any suspicious vessel exactly what the battlecruisers did to Harvest Joy.