Just got a pair of mavic rims in overall good condition, but with somewhat rusty eyelets. It's mainly on the surface so i guess it can be polished away. You think the rust could affect the strenght of the wheel when built up?

are you building with used rims or new old stock? if its surface rust it will come off easily with some oil and a rag, steel wool if you must. there was a time before rims had eyelets.

you can polish away for looks. rust on eyelets is rarely indicative of structural problems. I'd leave the rust if it's a commuting/utility bike. the crappier it looks, the less thieves are interested.
sounds like the rims are pretty old? I've re-built used rims before, and it's fine as long as they're reasonably round and true prior to tensioning (basically no dents)