I put 2.5% Benzoyl Peroxide on my forehead after I get out of the shower. I used to get horrible forehead breakouts to the point of always styling my hair with thick bangs, but after a few weeks with the BP I had movie star skin. The BP kills the bacteria in your pores and acts like a mild bleach, so it will probably lighten the pads inside of your helmet a bit. There is a small fraction of the population that is intolerant to it and will turn bright red if they use it. It's certainly worked better on my acne than Retin-A, and it doesn't make me burn even faster in the sun. The guy who runs acne.org makes a low-cost BP that feels nice when it goes on.

Other options are carrying antibacterial wipes to clean your forehead with after you take off your helmet, using a clean fabric layer between your head and helmet, and so on. Just make sure that bacteria won't be encouraged to grow between your head and helmet.