Ah, I see why it was wired that way. The heater must sense if the pump is on or not. Well that takes care of my thought process on the wiring. Yes, leave the pump and heater wires as is.
So IIRC, you will want to take the heater wires off the breaker and route them up to the timer (you'll need to extend the wires).
Next, route wires from the breaker up to the timer. This puts everything on your small sub-panel/disconnect/whateveryoucallit breaker. The house breaker is then only on the sub-panel/disconnect/whateveryoucallit.
This is what I would do.
And yes, danpik's idea to put your GFCI at the house panel is excellent. I missed that one, too.