My UK husband and I have visited the US twice since we've been married - we always head for the non-citizen line, but end up in the US citizen line because things have moved so quickly - we get waved over to that line. It's never been a problem and we've never asked anyone (we entered via Minneapolis once and Chicago the other time) and they've had the capability to do the fingerprint and photo, no problem.
We re-enter the UK the same way - he comes in the line with me, and it's never been a problem, basically the same thing has happened - they finish with the citizens quicker and we end up getting waved over into that line. This last time, the IO noticed my husband's UK passport and asked him what he was doing in the wrong queue. DH just said he was coming through with his non-citizen wife, and the IO just nodded, said it wasn't a problem...(Birmingham airport)
To me, it doesn't make much difference - one of us is always going to have to wait for the other if we go through separate lines...