seriously...you are way over thinking this.
It is fine. It wont "fail".
Remove the clips, you will never know it was ever there.
You are probably right due to it being inside the cab. Then again, maybe it won't start at a massively inconvenient time 6 years from now. It just depends on the environment, usage and amount of damage from the crap taps.
There was nothing wrong with any of the dollars he paid for the new truck, right? I think he's got the right to expect a truck that doesn't have damaged wiring. That's part of the advantage of buying new.
They could easily de-pin those two wires and run new wires that are not compromised.