I think it could be a good thing if the reactor could react to/ emit analog redstone signals.
Like emit signal depending on the energy within the buffer, so one single redstone output is enough to turn the reactor on and off.
Set the control rods depending on incoming redstone signal (its enough if its only reacts to signal strenghts 0-10). Choose whitch rod to set from that port.

The Redstone API is a flaming pain in the ass, poorly and inconsistently used in even Vanilla minecraft, and isn't consistently supported across different mods, so I'm going to avoid doing this.