I would have thought the same. But you could get around it by building your RE as a string and then putting that into the s///:
my $allowed = "pure";
my $re = "[^\Q$allowed\E]";
my $str = "p uuu+tr-ed";
$str =~ s/$re//g;
print $str, "\n";
Caution: Contents may have been coded under pressure.
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