Assuming OPs side of things is mostly true it sounds like:
- OP was working for a bad director, one so bad that they eventually got fired - Instead of placating this director and pretending to take their concerns into consideration, OP fights back more than other teammates (reading between the lines of the quote "However, given that I was far from John’s favorite (we never openly came into conflict, but I didn’t put the requisite amount of enthusiasm into jumping through his hoops to really get onto his good side)" here) - The director gives him a very poor performance review, that seems to have had serious impact on OPs career, team selection possibility, and personal finances, despite the director eventually getting fired
It just seems like a very high price to pay just to be able to tell yourself that you're not putting up with bullshit.