Funny, mine has become a night-pooper recently, too. It's annoying. Unfortunately, DD has been waking up so frequently at night lately that I can rarely discern the poop-waking from the others and we end up with a surprise in the morning. If I haven't washed her overnight diaper, I slather her well with a barrier cream before putting her in a disposable.
That said, we've been giving DD a probiotic lately and it seems like the night-pooping has calmed down, though that may be a coincidence.
Oh, and when DD has those times when she wakes all the way up at night, our best bet is usually NOT to try to put her back to sleep right away. I keep things dark, don't give her any toys or play with her, don't really talk, but I do let her do her little wakey thing and quietly assist her in doing what she wants to do. When she starts rubbing eyes/whining, then we try going back to sleep and it usually works right away. Whole process usually takes about an hour - way shorter and way less stressful than when I used to try to get her back to sleep the whole time.