To keep Ubuntu on the computer and get rid of Windows will require wiping Windows and reinstalling Ubuntu. But there might be another solution: if you can shrink the Windows partition (which will include the Ubuntu installed in WUBI), and thus get enough room to do a fresh install of Ubuntu (not WUBI), you'll then be able to access all of your Windows data (and Ubuntu WUBI data). At that point you'll be able to grab the data you need and want and move it to your new Ubuntu installation (or even run a backup from Ubuntu WUBI, saving the backup in your new Ubuntu installation), then delete the Windows partition and expand the new Ubuntu installation to take over that space, and then restore your backup.
I know that might sound complicated, but it's really pretty easy. Just one step at a time.