Hey there, I totally get wanting to simplify things and get rid of leaky hoses you don't use. That's a smart move to make maintenance easier down the road.
But just capping the lines at the control valve might cause a headache later on. The main thing to worry about is if someone (or even you, by accident) bumps that foot pedal. If the ports are capped, the hydraulic pressure has nowhere to go. It could build up and potentially damage the seals in your main control valve, which would be a much bigger problem to fix.
A safer and better way, I think, may be to "loop" the circuit. Instead of using two caps on the control valve ports, just connect those two ports with a short hydraulic hose.
This way, if the pedal ever gets pushed, the oil just flows out one port, through your new little hose, and right back into the other port, returning to the tank. No pressure buildup, no risk. You can then go ahead and remove all the old auxiliary hoses and the valve as you wanted.
Just a thought. Hope this helps you get it sorted out safely.