It should actually improve the performance of your A/C a small amount. A lot of modern cars have an automatic core bypass for when you max out the A/C.
Old Air Products makes a decent electronic bypass kit to improve AC performance, though it wouldn’t work to stop a leaking heater core.
The cheapest and easiest way is to use a double ended barbed fitting (you might need a size adapter) and merely plug the two heater hoses into each other end to end. Secure temporarily with a couple of worm drive clamps.
Be sure to set it up as an actual bypass that allows coolant to flow through the hoses to and from the water pump.
Do not deadhead the flow by plugging the hoses or installing shut-off valves. The TJ uses the heater core as the recirculation line, and by cutting it off you stop all forced coolant flow in the block until the thermostat opens.
If you do have to deadhead the flow in the tubes for whatever reason, drill a good size hole in the thermostat (I would do at least 5/16”) to use the radiator as the bypass to make sure there is some bypass flow. This is not preferred as it will take the engine longer to warm up, and performance, fuel economy, and emissions will suffer.
But deadhead the flow with no bypass and you risk boiling coolant in the block and creating huge expansion stresses as localized heating is not smoothed out by coolant flow before the thermostat opens.