When my husband (then my fiance) and I were applying to programs together (his for PhD, mine for MA), he knew before I did, and had to accept very early because of his fellowship. I called the department and asked for an early review, and they accepted me immediately. I think his acceptance actually helped me out a lot.
I've never heard of schools discouraging unmarried/civil union...ized partners before, and everyone I've spoken to who had a situation similar to mine had positive results, so I'd guess it's the opposite. I wouldn't give them too much information, though--just have your partner contact their departments and say that the two of you are trying to make decisions together but have your deadlines to contend with as a result.