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I'd lay 10-1 odds that if you weld it the weld will A) suck and B) cause even more cracking. Cast aluminum is a complete slut to weld, and it is somewhat porous so the weld will be contaminated with ATF as well.
Even if you could get it clean enough, and you managed not to melt down a nearby seal the case will likely crack even worse due to the rapid expansion caused by welding. The shape of the tranny case does not lend itself well to expansion and contraction caused by the welding.
If it were me I'd find another case and swap all the guts over.
Rene
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Yuppers, just like Rene said, cast aluminum is tough to weld. You need to have it under the proper heat conditions, just like cast iron. That means heating it up, keeping it up( /forums/images/graemlins/blush.gif ), and slowly cooling it.
Either a new case, or JB weld if that isn't a posibility.