There are a few things wrong with this encounter:

the Kithrak, Voss, if told we're the ones he's looking for, promptly gets on his dragon and flies away; "Ah, you have the weapon I'm looking for...I'd better get on my flying war crime and go-Baretha take care of them and bring me the weapon"; It's James Bond logic bordering on Austin Powers logic.

the conversation is started by Lae'zel but its beats are dictated by the PC, and we still have the issue of unclear motivations, between Lae'zel and the Githyanki and Lae'zel and the party. Lae'zel makes it clear that our lives in her eyes are pretty much forfeit, she tells us this explicitly and if you probe her mind you learn she views us already as monsters, so why she's so surprised by the patrols reaction isn't really clear to me.
But I think one of Lae'zel's character traits is naivete, slightly obscured by her coming from a very alien culture, maybe that's why people are so willing to follow her lead when it comes to the creche, despite a slew of red flags telling us that these fellows are bad news. Most of the corpses we find in the EA are killed by the Gith, and we see them murder a lance of flaming fist, I understand that nobody remembers Alderaan, but I'm still not sure how we can drive the point home better.

The encounter's placement on the map isn't a big deal to me, but some the logic around it are. I don't think following Lae'zel around like she knows what she's doing is reasonable for most characters, except another Githyanki.