The idea would totally work, but i don't know how to automatically remove any component of the reactor. You're using another mod than industrial craft?
I don't get either your "start timer".
As i got the pistons only pushing blocs & letting lava go on when the uranium cell is gone, you can guess i know a bit about redstone and detector cable
But i'm not using any mod permitting me to automatically remove a component from the reactor. I'd be glad to know one.