My water pumps have had a little filter built into them. After running the pump and getting nothing out of the tap, I remove that filter cap and dump out the water as well.
But your question brings up an interesting thought. Certainly the water pump is something you do not want to freeze, and what if you cut the output line and put in a T-valve with one input and two outputs. One output could be to the fresh water system, and the other to a short hose and a tap. Run the antifreeze into the water pump, and out the short hose, none will get into your water system. You can easily blow out the water system then, and not worry about the pump.