I just do it like this:
When the transformer is NOT receiving redstone power, it let's energy through to the mass fabricator. When the transformer IS receiving redstone power, it tries to send energy the other way, but since the mass fabricator doesn't produce energy, nothing happens.
Just keep an eye on how much energy you have in your MFSU and turn the transformer on/off accordingly.
it also works the same way when put on a eu storage like a batbox a lever will act like a on/off switch