I don't think Khadgar will be much at all in the limelight in Battle for Azeroth, and by that assumption I don't think Kirin Tor will play any kind of role either... except maybe near the end of the expansion when both Horde and Alliance clear their heads, realize they're being stupid, and band together to deal with N'Zoth ASAP.
So to answer your question: yes. I think both Khadgar and Kirin Tor are gonna be on Team Azeroth with Magni.