I tried this a few months ago using buildcraft gates without any luck. I also tried using Ender IO pipes and setting them to pay attention to Metadata... still no luck.
I tried putting a hopper under the MFE and having the MFE only emit a redstone pulse when it was empty, then using a NOT gate to reverse the signal so that it would emit a redstone signal at all times until it emptied out, which would turn the hopper on and suck otu the crystal... can't remember the issue but that didnt work either.
What I am trying to do is fill up crystals that are hooked to a railcraft boiler and turbine, then have a cart pick up the full crystals and drop off empty ones to be refilled. But I can't get the crystals to stay in the MFE until full, then get sucked out.