So just decouple it with a 1.5K resistor like I suggested. This way if the micro is trying to hold the SCL line up or down it is of no concern. You simply attach your in circuit programming driver right at the EEPROM SCL line and simply make sure your driver can source and/or sink the additional current that flows across 1.5K when the micro is trying to hold the SCL line in the opposite state as your in-circuit programming fixture trying to put it into.

Under normal operation the series resistor between the micro and the EEPROM will be almost transparent becasue SCL input to the EEPROM should be relatively high impedance.

Now if the micro is indeed an open drain output on SCL then you won't need this series resistor. But if it is truly push-pull, like you said, then add the series resistor and purge the normal SCL pullup resistor.

Michael Karas