Maybe wait for some rain to hit the area, i know it breaks the magnetizing effect on the toroids, not sure if it lowers the power of the VdGs as well. Otherwise you could try "sniping" them with some ranged explosive or something to hit their engines/shafts/whatever without harming the main structure, depending on how you built it. Maybe a rocket launcher. Or send a mining turtle in a straight line from outside their range until it destroys them. Or ic2 mining laser maybe.
But yeah, the VdGs are annoying, i made a whole redstone control system just for their engines and built the walking area out of their range to try to minimize the risk. I had the same issue with a single VdG i used on magnetic pipes at first try, i thought it could target the pipe above it but it didn't, so after clicking fast on the engine to set it up to max the VdG promptly zapped me to death, then exploded out of boredom after some failed attempts from me to reach it.
I'm sure that if there was some log about players killed by Rotarycraft blocks, the VdG would be more deadly than turrets or anything else, lol. It's very unexpected and surprising, can bypass all armor it seems, shoots through anything and the range makes it hard to escape once you make the mistake.