The tone of your question implies you've just been "victimised" by a pilot!
I have refused seemingly legitimate shipments in the past (at my previous places of employment) for many reasons. The segregation rules may have been violated; the package may have been damaged; the package may be leaking; the package may be of a radioactive nature that won't travel on a particular airplane because of distance requirements; the shipper may have "misstated" information on the declaration; a host of other technical reasons.
Unfortunately, during contract negotiations gone sour, many people do many things that irritate many people. One must be very careful when picking one's battles...