Is it safe to ground a pump house using the water line?
Short answer: This is a violation of the National Electrical Code.

Long answer: The Code has always required the grounding of metallic parts that may become energized. Your circuit to the pump house should contain an equipment grounding conductor. Residential systems have a voltage level that qualify under the systems that must be grounded in Article 250.20. A water pipe does not qualify as an equipment grounding conductor under Article 250.118.

If a ground fault occurs the water pipe will become energized. 

Have it corrected at your earliest convenience.