Well, when you chop an onion, the chopped up pieces aren't going to disappear, they will stay chopped up pieces. So if you don't like onion pieces just don't put onion pieces in it. FWIW I think using a whole onion for only a few cups of chicken meat is too much onion. I love onion but that seems like a large ratio to me. So that's probably why it tasted too onion-y to you. I would leave the onion out altogether if you don't want any onion taste, or put a little dash of onion powder instead.