Having a water pump seal go bad and put water into the motor is not a big deal. Seems like most around here have done it. I have not only had water pump seals go bad, I have drowned my bike under water and filled the crank case. Not too big a deal, but I would flush the motor with cheap, clean oil at least twice before filling with new expensive oil. Just my opinion.
Also something to think about, but if the WP seal is bad putting water into the oil, the oil level should go UP with a drop in radiator water. You said you were losing oil?
Brents347 Truckee, CA.
07 Yamaha R6
07 KTM 950 Super Enduro
04 KTM 250exc- plated two-stroke