The only issue that may create an incompatibility seems to be the IOREF pin next the 5V output pin which is extra on Revision 3 but not in Revision 2.
However, I just had a look at the board schematics and the shield does not use IOREF.
Pin 2 is extending IOREF
So, the shield should work correctly with the Uno Revision 2. As far as the extra pins are concerned, I would recommend not damaging them in any way. If you absolutely need to, then just try to bend them outwards very carefully.
The extra pins do not matter. Just leave them. If you really want, cut them off, but this will remove some compatibility with other products.
They should hang off the ends of the headers closest to the power/USB end of the board.