It was pretty obvious that Punk and the Elite could end up clashing. Both have VERY diffrent wrestling philosophies and neither are known to be people willing to compromise on that vision. Heck, the Bucks cannot compromise on that because it is the only reason why they became relevant. Disrupting conventions is how they got over.
Ironically, both sides see themselves are more important than they really are. Push Danielson correctly, put more emphasis on MJF, continue to build Wardlow (and do it better), feature FTR more, continue to elevate the Acclaimed, Garcia and Yuta. Do all that and you will have your own stars and you won't need the Punk headache. And, well, the Bucks and Kenny aren't mainstream draws.