What if you continue to match them, but not alter them if they are in your stoplist?

# assuming @stoplist
my %stop;
@stop{ @stoplist } = @stoplist;

s/(\w+)/ 
         ( $stop{$1} || ! defined $self->{$1}{val} ) ? 
           $1 : 
           $self->{$1}{val} 
       /ge;
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Might not be ultra-efficient, though.