## untested, just a guess
    my @path;
    foreach my $path ( split( /:/, $ENV{PATH} ) ) {
       if( is_allowed_path($path) ) { ## whatever that means...
           push @paths, $path;
       }
    }
    push @paths, "/some/other/path";

    $ENV{PATH} = join( ':', @paths );

##</code><code>##

     delete $ENV{PATH};
     $ENV{PATH} = "/path/to/tool;/some/other/path";