I like the idea of pressing seams open. When I started quilting it was a huge no-no but unless I'm using a fabric that the seams will show through why not? I'm going to give it a go on my next project.
I really don't know of a way to remedy your problem other than to re-press the seams when it's completed, right before sandwiching, I just did that and it worked fine. I do think that sometimes it's unavoidable though. (but not a big deal)