I wish I had a suggestion for you, but I wanted to post to tell you that we're in the same boat. DS spits up a lot when I hold him over the sink--and not just for pooping, but for peeing, too.
My guess is that it's pressure on their tummies from holding them that way. If that's the case, I guess using a potty might be better? Please chime in if you have an answer! In the meantime, know that you aren't alone.