Scrubbing the rocks will not likley prevent the algae from coming back. I was in the same situation as you a while ago. My solution was taking the rocks out and blowtorching them untill I was sure every bit of algae root was gone. This is an extreme measure.
The algae will pull nitrates and Po4 out of the water but it will not fix the main source for the Po4. It will keep growing and growing leaving you an unhappy camper. My suggestion would be to pick up a phosphate reactor. Like the MR1 made by nextreef. And run some neozeo media. This will cut out Po4 as well as Nitrates. In my case eliminating the need for water changes for almost a year now.
Next Reef MR1
NeoZeo