They will rust, it is normal.
Seals are easy install. You do not need to take the diff cover off. But since you're down there, when was the last time you changed the fluid? What about the u-joint? If you're going to pull the shafts you might as well get the other easy stuff while you're there IMO.
'78 Scout SSII - 345, 4 speed, SOA, locked, 33's...
'06 LJ - 3" lift, 33x10.5R15's, Discos, TrueTracs, 4.56 gears...
'80 Scout II, '89 YJ, '79 Scout II, '93 YJ, '01 TJ, '00 Cherokee - all lifted, most locked and all wheeled