Yeah, that is 99.99% sure to be algae. Looks like your Hydroton is getting too wet too high.

Keep the top layer either dark or dry (or both) and you won't grow algae. Obviously, with a top-feed system like yours the dry part can be tough. I'm pretty sure one of the beneficial bacteria type of products would kill it - start eating the algae (turning into food for your plants) and since it's alive it multiplies and keeps going.

Assuming I'm right on that... I haven't tried it on algae myself.

The plates sound like a good idea. Just cut to the center, round out a hole for your stem, then slip it over the top of the pot. You might want to go with a thicker plate or several plates - if memory serves they're not exactly light-proof.