No, that wouldn't damage it. Even on the outputs you have to do some pretty diabolical things to hurt them.
The 9396/6401 is even more well protected. Something else is up or it was divine intervention and the ECM did a belly-up. I really doubt it.
Even if the ECM was cleared from disconnecting the battery it shouldn't blow black. Rich on a cold start up, yes, but not black unless it's just clearing the excess gas from the engine. That should only last a fw seconds. You knocked something loose somewhere.
[This message has been edited by TK (edited 11-01-2003).]