It won't prevent it from being fitted back into an A2000. Some dust may get in through the hole, though, but you could just tape over that.
I recommend removing the metal sleeve from the drive before cutting/grinding the metal away. Little metal particles are a bad idea inside the drive. :-)
There's one phillips screw in the rear top and two bigger phillips screws from the sides. Take out the front plate from the drive, remove those three screws and then the drive mechanism slides out of the sleeve.
Also please note, that there are several kinds of tall A2000 drive.. You ideally need one of the later drives, 1988/1989 or so. You should compare the drives side by side a bit first.