Yep. At the very least, just make everything a civil union that any two consenting adults can enter into. Religious people can still get "married", it just has nothing to do with the government.
Why limit it to two? I say allow any amount of people in a civil union, or allow one person to have a civil union with multiple people separately. It's mostly for visits in the hospital, parental rights, stuff like that.
Of course, that makes residence/citizenship based on relationships complicated, but that's mostly an issue caused by closed national borders being a fucked up concept in the first place.