I did the non hostile option on my first playthrough. Lae'zel says something about teh creche being in the area somewhere and finding it another way. It's probably in the mountain pass beyond where we go now anyway.
My latest playthrough I went out and scouted the Gith from above from the bridge It was pretty early in the game (2nd level I think). I did not have Lae'zel in the party yet - not even in camp. After scouting for a few minutes I decided to come back later and headed back east. Then a journal update appeared and said that Lae'zel had died. So I guess you don't even have to have the actual encounter to affect the story. I was just in the vicinity. Guess she won't be joining my party any time soon in this go-round.
I had the same problem! Lae'zel wasnt in my party. I had to recruit Lae'zel in my party, item popped up in my inventory, clicked it and it started the cutscene.