From their GPRS shield wiki:
Note: A4 and A5 are connected to the I2C pins on the SIM900. The SIM900 however cannot be accessed via the I2C .
Yes, it would make sense to me that you would disconnect those pins. I would suggest that instead of cutting any traces that you simply cut/desolder/remove the A4/A5 pins from the GPRS shield. Two little snips and you're done, and if for some unknown reason you need them back you can replace them.