I've read the other thread, and this one, and I think we're all overthinking it.
In SM1, the scriptwriters are obviously setting us up to encounter the "Gwenhyvar". We hear a ghost story about an Exeter that was captured by the Kilrathi, being used to lure pilots to their doom, and then the next mission, we're sent out after an Exeter that turns out to be captured by the Kilrathi, trying to lure us to our doom. Obviously, it is the Gwenhyvar! Or at least, it seems obvious that that was the intent. And Blair even confirms it by saying that it was the Gwenhyvar that he encountered.
So what about the Johan? Does this mean that the Kilrathi needed to destroy/capture her to lure Blair in? Not necessarily, though everyone in the other thread seems to think so.
Scenario: The Kilrathi did indeed capture the TCS Gwenhyvar in tact, with or without fighters. They have also managed to acquire Rapiers. Maybe these were on the Gwenhyvar, or maybe the Gwenhyvar capture was before Rapiers were out and the acquired them from elsewhere. But it makes sense that if you are using a Terran capship to infiltrate Terran lines or lure other Terran ships into traps, you want to equip it with Terran fighters. And you obviously use the most advanced and up-to-date fighters you have managed to get your hands on.
Now, they know the Claw is following their fleet, and they have their captured Exeter handy. They maybe know the name of an Exeter that is patrolling nearby the area. There's no need to destroy or capture that Exeter...all they need to do is send their Exeter out and have it radio the Claw claiming to be the Johann. The real Johann is presumably maintaining radio silence, or has even patrolled on to a completely different patrol station, and probably was fine the whole time. The Claw gets a distress signal from an Exeter claiming to be the Johann, and sens pilots out to help.
If I know a given ship is in an area, and I get a distress signal from a ship of the same type claiming to be that ship, in a different location but with an explanation of how it got there, I probably believe it and send pilots out to help, especially if the situation is dire and it would take hours/days to try to verify that the ship is indeed what it is claiming to be. If the Claw thought the Gwenhyvar was the Johann, they would not spend hours and break radio silence trying to raise the real Johann on its patrol station just to make sure that the distress call they got was real.
As to the reference in SM2, it could be as simple a matter as whoever wrote the game script getting mixed up and using the wrong name--the name that the Exeter was pretending to use instead of what it actually was. Or, if you perfer an "in game" explanation, when Blair said "the last wing from the Johann", he could have meant "the last wing from the Johann incident", i.e. that time that they got fooled into thinking a ship was the Johann.