Yes, capping them is just fine and the way you did it will work, BUT...
I would rather see you plug those heater outlets off than have hot water from the engine recycling right back into the water pump. If you don't want to try unscrewing them from the manifold and water pump to install pipe plugs, you can buy "Bypass Caps" (heater hose outlet caps) at NAPA, rubber covers for the heater outlet bungs. That way hot water is forced back through the radiator.
They sell them in both sizes for your outlets - 5/8 and 3/4 if I remember right.
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