It can work ... a few you may want to consider ...
* when you "peel" it off, careful or you could disturb, even pull the stitches
* you may also end up with crumbs of the paper in the stitching
* FMQing on the sandwich with paper on top will have a different feel to it than without
* some use tissue paper rather than the "hard" freezer paper
As already said ... do a trial run first to help you feel good about it and to get your technique figured out, before committing to your "real" project.