>Some of them seem remarkably frivolous:
As are most patent filings (including some of my own)
As are most patent filings (including some of my own)
Why file them, then? (The fact that you admitted to it suggests you have a valid and ethical reason to do so.)
"Don't hate the player, hate the game."
If I join up with the Nazis, the Nazis are stronger.
If I file a patent, one more idea might go unclaimed by a major corp. Unless I am litigious on their level, the patent will hurt fewer people.
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.
I believe the context was software patents.
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.
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.
That sums it up for me.
(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.)