Well, there is a mechanical water pump, and there is the electric water pump. Parts are listed online for the 3.0 X5; this is a booster pump, mounted on the firewall, intended to increase flow through the heater core. It is the type of device that could cause a current draw if it malfunctioned.

You may still want to take it to another dealer, but realize that the one you are working with may actually be right. He knew there was an electric water pump. I didn't, but I found the part in 30 seconds on the web.

It would be normal for the dealer to check the full charging system during the repair they did, you can ask them if they did so. The red light you see, is it on your charger or the dash? If it is on the dash, then yes, contact the dealer. If it is just the light on the charger, run the vehicle for awhile and see how it works.

__________________
2007 X3 3.0si, 6 MT, Premium, White

Retired:
2008 535i, 6 MT, M Sport, Premium, Space Grey
2003 X5 3.0 Steptronic, Premium, Titanium Silver
2002 325xi 5 MT, Steel Grey
2004 Z4 3.0 Premium, Sport, SMG, Maldives Blue