Erythromycin at 1/4 dose ( found in Maracyn ) will rid the tank of diatoms. From there you just have to stay on top of water changes. As far as cleaning rocks... soaking in a hydrogen peroxide solution ( or you can use Prime, just more expensive ), will kill most algaes/ diatoms. I don't normally use chemicals in my tanks, but I do use the erythromycin treatment for new setups.
Interesting.. I have never heard of using EM to combat Brown algae aka diatom.
my understanding of diatoms is, once the silicates have been reduced they no longer can form their shells.
I do know it works on BGA as it is cyanobacteria. EM of course is an anti biotic and effective against BGA.