This hack is the first thing that comes to mind (untested):

( my $code = do { local $/, @ARGV = './conf'; <> } )
  =~ s/\$/'$'.__PACKAGE__.'::'/eg;
eval $code;
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It assumes that all variables are scalars, and that there are no stray $'s in the file. This would put the variables in the current package, but so what? The crucial question is: what are you planning to do with these variables?