Hmm... Not sure about that. I have in the past (many times) "hot plugged" a stick with bad SPD, while the machine is idle at open firmware or boot menu, but that is a TERRIBLE idea and you should not do it... Working on under warranty hardware and with essentially unlimited replacement parts sometimes makes one take stupid risks... Though fwiw, I have never had a problem.
also I never tried DFA with a DDR Mac... MDD do seem very particular about SPD though, it took me three tries to get a profile which would not intermittently freeze my machine (and I really don't know what was different... It wasn't something obvious like CAS latency or speed...)
Rather than desolder EEPROM, it would probably be easier just to solder 3 or 4 small jumper wires or hack up an old slot to make an adaptor.