A work around I have found in the desktop version is to put an exit script; statement at the end of the first section (Main) where the SET statements are. Then reload and save. Then comment out the exit statement and reload. The QVF file should be smaller. I don't know why this is happening but it's a pain for large apps that you want to put on the cloud and you need to keep under 50MB.
Your answer reminded me to update this post. Altough i haven't tried your solution, i noticed that uploading the app to the cloud greatly reduces the size of said app. In my case it went from 25 MB to a little over 2 MB. I'm not sure why this happens, maybe it's some sort of optimization that occurs during the upload, but for now it fixes my problem.