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.
