How bad is it for a couple to often attend different churches (but maybe share on some holidays and other days)?
It depends on the individual. It's not ideal, and (IMHO) adds another layer of difficulty to the marriage. But it really depends on what your non-negotiables are. It is very important to me that my husband and I attend the same church, and share the same faith. It may not be that important to others. Anecdotally, friends have told me that it gets a little lonely going to church by yourself, and perhaps not being able to participate fully in the life of the parish. Also, with kids, it gets even more difficult.
I grew up in a family like this. While my mother and father loved and respected each other and had a wonderful relationship, it was still hard on all of us being split between two churches. Maybe that's why it was so important to me for my husband and I to share the same faith. Also, I don't want my faith, which is the deepest, truest part of me, to be a subject of constant negotiation and compromise. I want to be able to share that part of me fully with my husband.