I just think it would be an odd fit to put a great character driven wrestler who is great on the mic with a manager of the same irk, its like one of them would have to give way. I except that Mr Perfect and Rick Rude had Heenan but chances are they would have got over without him. If you are going to stick Heyman with Punk then maybe build a heel stable rather just make it them two alone.
I think maybe a feud between the two might be better, you could do it reality base where Heyman slates Punk for giving up on his values for more money and a main event slot.