-Leave the pipe off but leave the wiring harness and vacum line plugged. Will let a little extra air into the throtal body but doesn't seem to cause any problems.
-Unbolt the EGR, remove wiring harness, plug the vacum line with a screw and make a small sheet-metal plate to cover the hole in the TB. No negative effects other then the check engine light will most likely never shut off.
Just noticed you were running a turbo so I would definately go with removing everything and making a plate to cover the old hole. Dont' want any high psi leakage