If you go to my MEL page you'll find a hideSelectedFaces script. you could always try that... it was written for 4.5 but it should work on any version of Maya..
http://www.naughtynathan.supanet.com/data/mel.htmhttp://www.naughtynathan.supanet.com/data/mel.htm
I've never used the bonus tools so I can't say that my "hide faces" MEL is any better but it may be different enough that it'll work for you where bonus Tools didn't...
I've just checked my page, and the hideSelectedFaces.mel currently there is an older version, by all means try it but I've got a newer, improved version ready to upload (when i get home tonight). so don't forget to check back tomorrow!
:nathaN