sounds like you need to run it really clean with a copper brush. clean it up really well then shoot it several rounds or whatever you want to shoot, then clean it up really well again.
I think you should be fine. as will any metal object rust can occur, just make sure you store it in a dry place.
if you are putting it in a gun case to store it the gun case might have moisture in it, either dry it out really well or buy a new one.
post pictures as well if you can, it will help out so we can see how much rust is really there