One of my A1200's had a full set of clockport pins on the motherboard. I think I just waggled them off with a set of needle nose pliers - They came off easily, very neat, and flush with the motherboard header...just the two required pins of course. Clockport cable then fitted perfectly.
With the plastic frame around the pins, I doubt you'd damage anything. Otherwise, someone handy with soldering equipment can remove them easily.
