Actually, stainless and aluminum don't go together very well. Eventually the stainless screws can be become difficult to remove or could break in place. Stainless screws in aluminum should be coated in anti-seize compound to "break" the galvanic connection.
We should keep in mind that there are different grades of stainless with various levels of corrosion performance. For example, not all stainless is non-magnetic.
Corrosion of stainless parts isn't (usually) rust, but pitting. I used stainless threaded rod for an antenna bumper mount that I fabricated and the stainless appeared to rust on the cut ends, but is more likely bits of steel from the hack saw blade left embedded in the cut end.
I'm told that you can also harm the stainless performance by overheating the stainless during the cutting process but I don't know if hacksawing it qualifies as overheating.
It's just me, but I'd look elsewhere than the screws for the source of rust.
Quando omni flunkus, moritati