First, how likely is it that an electrical problem like this can happen during the shipping process?
Highly unlikely. Assuming your diagnosis is a bad pickup, even more unlikely. My first guess would be bad battery or disconnected battery, or, if the pre is on a circuit board, it dislodged and either broke off a wire or a trace was broken, like where a wire is soldered to the board. I would take a magnifying glass to the wiring, and look for broken or cold solder connections. Is the battery secured in a clamp, or is it flopping around loose in the compartment?
Second, in the process of trouble-shooting the problem, once the pickup became suspect, I had removed the panel to the electronics cavity and took a reading with my multimeter. I'm not an EE, but I've been an electronics hobbyist for years (retrocomputing and vintage arcade games, mostly). Being cautious and inexperienced with troubleshooting these things, I was guided over the phone by my instructor who is also a guitar tech. Because of this invasive method of diagnosis, the seller is now claiming that the bass is no longer in its original condition, and thus he shouldn't be held responsible for it. (Never mind the fact that that the problem existed before I did this.)
Sorry, you did not do anything wrong, except to assume that a multi would diagnose a bad pickup. The only real way to diagnose a bad pickup is to disconnect then test it for resistance. The cheap buy effective way is to tap lightly on the pick up with something metal, like a screwdriver. Basically what you tried to do is the equivalent of trying to test a resistor in circuit. Your defense to his dodge is that it may have well been that the battery died in transit, or was shaken loose from its terminal, so, you would have to open the bass to check that out. BTW, did you check to make sure the 9v is getting to the circuit board? You should trace that from the battery, and do a continuity, both + and -.
So, given the dodgy state of the sale, did I cross the line?
No. But the problem is that a bad pickup has to be tested out of circuit, and that's the rub. If it were me, I would be looking for cold solder joints, or broken wiring first. Does the bass have a passive mode? Some basses, you can plug the 1/4" cable in half way, and get a weak, but passive signal, which would then eliminate the Pick up. But my 2 cent opinion is I doubt it's the pickup itself.