Note that safe mode is largely useless. Most ISPs that offer Perl also offer other scripting languages (mostly Perl), and these other languages don't have the equivalent of PHP.
In other words, if PHP's safe mode won't allow vandals into your web presence, they will simply use Perl.
Also, safe mode prevents scripts from creating and using directories (because they will be owned by the WWW server, not by the user who uploaded the PHP script). So it's not only useless, it's also a hindrance.
The only realistic option is to bugger the Apache folks until they run all scripts as the user who's responsible for a given virtualhost or directory.