I've not had this problem on my roof, Dene, but if I did, I'd try to clean away the corroded area first with something like a Dremel grinding bit. I'd do this to get the aluminum away from the other metal underneath that is causing the galvanic corrosion. Then I'd use either EternaBond tape over the cleared areas or, I'd fill the holes with Lexel caulk (which you can buy at Ace Hardware or online). Lexel is an adhesive caulk that can be painted over. Dont use a silicone caulk!
Thinking about it, I'd probably try the caulk approach. Then, I'd coat the entire roof with a white elastomeric paint (which you can find in Home Depot or Lowes). I think this would make a very permanent, invisible repair.
- Jack