If Muldaur got more money it's because she had more TV experience than most of the actors on the show (except for LeVar Burton). And she earned it. She never portrayed Pulaski as anything but a class act and a formidable presence...which is what a CMO should be.
As far as being "friends" with Roddenberry, hey, the guy did fool around but there is not evidence to support he fooled around with Diana. Not every cheater cheats with every woman he meets.