Look into the hydrogen peroxide method for killing algae. Basically you buy some H2O2, and one of those baby syringes for dosing medicine, turn off all the flow and go to town carefully squirting the algae. It will start to bubble and fizz almost immediately, then die. This method has worked great for me and hasn't hurt any shrimp or fish. The byproducts of the h2o2 reaction are just water and oxygen, and it begins to break down immediately when exposed to light (hence why it always comes in a brown/opaque bottle).