I would not weld. Rust hole is small and can be rust proofed and sealed. As long as no moisture can get to it, it will not rust further. Buy this
DOW BETAPRIME 5504G ALL IN ONE AUTOMOTIVE URETHANE PINCHWELD PRIMER | eBay first.
Lightly wire brush the pinchweld frame to remove loose paint and rust, degrease frame with Brake Clean, brush entire pinchweld frame with the Pinchweld primer, use 5 min epoxy to fill the primed rust hole and smooth it out. Make sure the FSM glass rope-in procedure is followed or else the job will not come out right.
You do not have to buy the primer since the glass shop should have it and use it as part of the glass install, if he don't mind waiting 15 minutes to let you apply the epoxy.