Everybody is so dependent on computer diagnostics and swapping parts that there is no ability to use tools like a multimeter, oscilloscope, wiring diagram or basic mechanical troubleshooting knowledge to diagnose a problem. You could check for power to the pump when the bike is starting or physically remove the pump to see if it's turning. A clear bulb or flow meter inserted inline with the fuel hose would tell you if fuel is flowing. BMW uses standard quick disconnect fittings (or at least they do on my 2008), so doing so would be easy.
If you doubt the mechanic or suspect a bad wiring harness, you need to first confirm that either the pump isn't getting power or that it is pumping fuel.
If you doubt the mechanic or suspect a bad wiring harness, you need to first confirm that either the pump isn't getting power or that it is pumping fuel.