It shouldn't hurt anything. The heater core is a separate system from the engine cooling, just uses the same coolant.

I had to bypass my heater core because it's leaking, so I just pulled the hoses and used a nipple to connect them together. I drained enough coolant to not make too big of a mess, then filtered the coolant through a paper towel to get the rusty bits out, and re-used it. $2 for the nipple and didn't have to buy any coolant.