Chris has some excellent info in his thread about some amazing acid proof paint specifically for battery boxes!
Seriously....One thing you didn't mention was if it is structurally sound. It has been a while since I looked at your car, but I seem to recall the (small) battery having a good solid mount. If the structure is weak enough that its ability to anchor the battery is in question then a proper weld-in structural fix is in order. If this is purely cosmetic and for water proofing, then I'd say the seam sealer and paint fix is plenty. If you "tack" weld any metal in place you must be certain it is fully sealed or you will just make a rust sandwich that will get much worse in time. Another option for a non-structural fix is to properly sand/prep the area and then fiberglass some cloth over the holes before a final painting.
Eastwood and Auto Body Toolmart should both have the sealers, etc. you may need.
http://www.autobodytoolmart.com/
http://www.eastwoodco.com/