If a professional hockey player thought checking made the game needlessly violent, that wouldn't mean they could stop checking and remain competitive in the game they loved. The pragmatic option would be to keep playing the game, checking included, and advocate for change.
Yes, having your employer file a patent on your work (whether you want them to or not) is very much like taking part in the killing of humans through starvation, experimentation, and gas chambers.
While his comparison was clumsily drawn from Nazi participants, I think we can agree that the idea of blind participation is something worth criticizing. The reason corporations wield so much power is because everyone is willing to undercut everyone else.
Fair enough (enough to click the up arrow for a point well made), though I don't think participation in the patent system is quite as clear-cut. Gassing Jews? The vast majority would agree that this goes to the far end of the "evil" scale, if not defining the maximum of that scale. Having your employer patent your work? Meh, I'm pretty sure opinions will fail all over the scale, including the "good" end or at least the "still better than kicking puppies" part of the scale. For instance, I personally find software patents to be pointless and perhaps suppressing of innovation, but I don't get terribly rabid about it. But you're right, blind participation is certainly worthy of criticism, even if I don't necessarily agree that any participation is wrong.
How about drug patents, resulting in thousands of deaths because people in the developing world can't make and afford cheap alternatives?
And no, those patents (and the inflated prices) don't happen just to overcompensate for the "cost of research/FDA approval". The drug company often still has healthy, or rather ridiculously large, profit margins, on top of these costs.
They can file and be granted a patent on your work against your will. The system specifically accounts for companies that need to file a patent on the work of a "non-cooperating inventor".
As an employee, your refusal will probably get you fired (since you probably agreed to cooperate with patents in your contract) and burn bridges, and all it does is force them to spend a few extra hours on paperwork.
A previous employer wanted to patent some of my work, and I tried to use this as leverage to get them to implement something like Twitter's "Innovator's Patent Agreement", Google's "Open Patent Non-Assertion Pledge", or Paul Graham's "Patent Pledge" - only to find out that I didn't really have any leverage. I at least did manage to get it discussed, but ultimately it was rejected. This was a factor (though a minor one) in my decision to leave there.
"I was just following orders" is not just about purges and/or the holocaust as you imply (something the parent didn't explicitly state).
It has been a standard excuse in tons of other, smaller scale, wrongdoings.
Besides, while having your employee file a patent on your work is not similar to those cases you mention in the scale of harm it causes, it's very much the same exact excuse used there.
Because you're confident that your employer will only use them defensively, and because the system is broken enough that it's genuinely advantageous to good people to have hopelessly vague patents that appear to a judge to cover their inventions.
(That said, my own patent applications probably went to the highest bidder after the sponsoring employer collapsed. So maybe I shouldn't have been so confident they'd remain in good hands.)
The question of future control is why, being involved in patents without some form of contract in place that prevents abuse being in place, bothers me. I maybe trust current management not to be dicks, but trusting all plausible future management not to be dicks is naive.
As are most patent filings (including some of my own)