People get a divorce for lame reasons all the time. And Amy Pond struck me as someone who's not really fit for marriage, especially after going on adventures with the doctor. It's why I never really cared about their marriage(no matter how hard they pushed it as some kind of romance that will outlive time or someshit). To me, it was just a plot device to get her to be the Joseph for River. She was a companion first and a married woman second.