This is a known glitch with GregTech and Buildcraft pipes. It is fixed in 1.5.x version of GregTech. The cause is the GregTech machine tries to pull energy from the Buildcraft energy pipe and if it does not have the MJ upgrade already installed it will crash minecraft. The solution is to Backup your saves. Then MCEdit, or use a similar program, out either the GregTech machine or the Buildcraft pipe connecting to the GregTech machine.
If you want the GregTech machine run off of MJ instead of EU then place the GregTech machine somewhere else in the world. Add the MJ upgrade and then loss-less wrench the GregTech machine and place it where you want it. The GregTech machine will remember that it has the upgrade. If you are trying to run Buildcraft energy pipes next to the GregTech machines try using RedPower micro blocks to block the connection to the GregTech machines. Note I'm not sure if the micro blocks will stop the GregTech machines from trying to draw power it is just a guess.