What you are doing is not UN-common, we often shoot 1080 and edit in a 720 sequence. This allows room to move, cut in, etc. Works great.
But, you need to shoot progressive in 1080, like 1080/30p or 1080/24p
and then edit in 720/30p or 720/24p.
So why not res up the problem shots a couple of pixels and eliminate the issue?
Chris