The fact one partner prefers Candidate A and the other prefers Candidate B isn't that big a deal, nor is party registration. However, I think people who have major differences on political issues probably have value systems that are different enough to cause problems in a relationship. It isn't a deal-breaker -- I think James Carville and Mary Matalin are still married -- but it's one more thing that can make it difficult.
It's like religious or ethnic or educational differences.....not reason to avoid a relationship, but a potential pothole.