I don't think it is safe to use other than spot treating. I would spot treat just a little bit every day to give it a chance to break down. If you get too much in there at one time, I am sure the algae won't be the only thing dying.
I trim the roots all the time on my Anubias (all the really long ones). I do always leave about an inch or two. The roots on an Anubias are just to anchor the plant. They do most of their feeding through the leaves.