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While hydraulic systems in general don't like particles of any kind, unless you put a huge number of miles on your car with the pump full of ATF, the wear difference would be small. There is also a magnate in the pump that collects particles. Seems to work well as it is always coated in particles when I've rebuilt pumps. I'd just flush it if the pump isn't leaking.
BUT, have you run the pump dry very often? Makes a pretty good noise so would likely wear VERY quickly.
well its pretty straight forward, pull the hoses and let them drain. I did pull the alt. to clean it up to(why would some paint it blue), clean it up and spray down with breakclean, let it dry and paint. I will be putting it back together tomorrow or sunday