Is there a way to turn of Behemoths somehow? From the my point of view because of Behemoths endless space 2 is loosing there faction uniqueness which I would like to keep. 

I think you can only turn off the expansion itself. Or change the presence/absence of the behemoth quest.
I also had that opinion a while ago but more in terms of balance, but then Behemoths got patched up and became smth close to what theyre supposed to be. I also find them to be one of the  few turntables for losing players. And lorewise things bother me only until I use my imagination to justify them. A neat approach I would say ;)