Oh, I've always played with Sneaky AI on actually. I will definitely turn that off from now on, quite curious on how ranged-enemies fare after I turn this off.
I think you should not force disable the option if there is some improvement to keeping it on for certain missions. More freedom is better, even though a natural outcome is misunderstandings like these (which is probably 100% my fault). I turned it on mostly because I like the idea of having aliens and cultists take care NOT to stand in the open, but I'd rather not have that in detriment to the creatures being even MORE suicidal.