Just to make it clear that I know this:

A premature optimisation is a Bad Thing

Now, I'd like to oberve that you don't really need two separate hashes, but only the dictionary (or the exclude, if you prefer) one. Basically, words that were already seen (either because already present in the output file, or because you see them as you iterate over the INPUT ONE) are to be excluded, so you can mix the two sets. The consequence is two-fold:

• you have a single hash access instead of two, which is hopefully better;
• you don't waste resources auto-vivificating the %$exclude hash.

Update: corrected the auto-vivification beasty comment. I wonder how much wrong assumptions I've got inside my head - at least the magnitude order.