Technically the muffler is not part of a vehicle's emissions system. The only concern is that the muffler not have holes large enough to suction oxygen from the atmosphere into the smog machine's tailpipe sniffer during the smog inspection. If this should occur, the smog test will be aborted for excessive dilution.
Repairing the muffler as you've described should prevent oxygen dilution. A smog technician should not fail your Chevy Metro on the basis of a visual malfunction due to the muffler being patched.
