If you have a mod with logic gates, such as any Redpower replacement as suggested by Korlus, you can do a nice compact thing with a toggle latch. If you only have vanilla redstone at your disposal to build a handmade toggle latch, I wouldn't bother - those things can get pretty large (think 5x5 redstone circuit).
Set your MFSU to "emit if partially filled". Patch the signal through a NOT gate to invert it. You now have a setup that delivers a high signal whenever the MFSU is empty OR whenever it is full. The toggle latch is a special circuit that toggles its state back and forth everytime it receives a high signal. Can you guess where this is going?
Connect your signal from the NOT gate to the toggle latch, and connect the output of the toggle latch to the reactor. Now you must prime the system: make sure the MFSU is partially filled, so that the NOT gate sends a low signal and the latch is dormant. Then toggle the latch manually, for example by placing a redstone torch next to the wire between the NOT gate and the latch. Just one quick pulse is enough, then you can (and must) take the torch away again. You will see the latch toggle to high, and your reactor will start running.
It will keep running until the MFSU is full. Then the MFSU stops emitting, the NOT gate inverts that to high, which toggles the latch, which turns off the reactor. Then the MFSU maybe stays full for a while, or maybe it starts draining immediately, it doesn't matter. What matters is that at some point, the MFSU is no longer full, therefore drops back into its "partially filled" status and emits redstone. The NOT gate inverts that to low, which takes the signal off of the latch, making it ready to receive the next high pulse. That comes when the MFSU is completely empty, and thus no longer "partially filled", which has exactly the same effect as when it was completely full. Again the latch is toggled into the other state, this time turning the reactor back on.
As long as no wayward redstone signal interferes with the MFSU, the reactor or the line in between, this system will stay perfectly self-regulating for all eternity, and you don't need an expensive second MFSU to make the redstone logic work. However, beware of one corner case: if the reactor is on, and runs out of fuel, and the partially filled MFSU also reaches completely empty before you replace the fuel rods, then the system will toggle itself permanently off. You will need to prime it again as you did when you first constructed it.