I'd be very wary about doing this completely automatically. There's nothing stopping someone from calling an arbitrary method $somePkg->$someMethod( "blah" ), with either of those variables set at runtime. You'll need to be looking very closely at all of the code, otherwise can't be sure that there's not some code path that's setting $somePkg to something you've removed since you never saw it called.

Update: And a similar caveat for plain subroutine calls if there isn't a use strict; there could be &{"${somePkg}::$sub"}() calls to who knows what. Granted this probably unlikely (I wouldn't write code that way), but be aware of the possibility.

Update: You should probably get your boss to spring for a copy of Refactoring (ISBN 0201485672) as well.