Not much help, but if my hosts said that, I would transfer out to a hosting company with the know-how and flexibility to meet my needs. Seriously.
There is loads of talk about being able to set safe-mode on a per/site or per/directory basis, through php.ini or .htaccess files, but the .htaccess doesn't apply to safe mode, and php.ini can only be set by your hosting providers.
I'd transfer out.