Did it break internally? If there is not metal contamination on the inside of the old motor you should be fine. If there is already contamination the pump is probably ruined already anyway.
There is no way to flush the system. There is a setup that you can hookup in one of the high pressure lines with a high pressure filter and run the pump in a certain direction and it will filter all the oil on the high pressure side of the system. The kit to do this is very expensive and most dealers probably dont even have one and most of the manufacturers dont recommend for us to buy it...
The only way to flush it would be to remove the pump, disassemble the pump getting all the oil out. Flush the lines and put it all back together.