Don't sweat, duckman. Fungus gnats're annoying and tickle up the nose. That's about it. They won't hurt anything except a little pride for not growing the perfect crop.
Next time, you have a few heads up. The perlite layer sounds like a great way to treat an in utero infestation.
An ounce of circulation is worth a pound of cure. A pound of cured is priceless.