I would suggest trying an even lower bit rate for MP3s, and comparing the MP3s to the WAVs through a typical sound system that you would use at a gig and see if you can hear a difference.
There's no technical limitation preventing you from using WAV files in BandHelper, but the practical reality of syncing 40 MB versus 4 MB for every recording makes a big difference. I could possibly start a new account option for more file storage, but there's nothing I can do to make the files upload and download between your account and your devices more quickly.
Also, if your WAV files are already in iTunes, you can easily convert them to MP3s. Select all the files, then go to File > Create New Version > Create MP3 Version. Then you can right-click one of the new MP3s and go to File > Show In Finder to access the new files.