TBO. Your aquarium is very young and not mature enough at the moment to help sustain that acro properly. It will be a battle, but stay on top of it as you are. Keeping the algae down is a good Idea. A light brushing at this point will not hurt things anymore. The algae is winning the battle at the moment. Try not to harm the flesh if you can. From the looks of your aquarium, its still going through break in period, so the algae will come back fairly quickly. You may want to dip to help it.
You need to concentrate on stability of the tank. Unfortunately you will have to let the aquarium do its thing and go through the process. Once it becomes more mature. The areas will be able to heal on their own without algae issues. That just seems to be the phase you are going through right now. With allot of algae, the coral will not be able to heal properly.
I scrub my coral frag plugs on frag rack that get algae with too brush with no issues, but there is not algae on the coral. If you get algae on a coral on a branch per say.....its best just to cut that branch off and let if heal. In your instance if you did that, the algae would succumb the area and continue to kill the coral. You are on your way to stability, but it just takes time. Keep the coral as clean as you can as you get your aquarium into check. Good luck.