When I need the cart to stop after it takes off I have to run ahead of it, break a track out and lay down an advanced detector rail. Then to get it going again I need to apply redstone to the advanced detector rail and after it's on it way again replace the advanced detector rail with the one that was there before. Seems a little too much. There are several other times when you just need it to stop and always running ahead of it to lay down a advanced detector track is a pain.
The chunk loader will not activate when engine is disabled and forces you to use a module toggler.
Just turn off its engine. I don't see what the problem is.