Depending on the job, you can likely be fired without cause anyway. You can pretend to not poke the bear, but in a place that plays power games like that, it doesn't really matter.
Presumably performance matters above all else (although it likely doesn't in such a place). If Emacs actually makes a meaningful difference, then just use it to do your work more efficiently.
You can run a batch/shell script, right? Of course you can. Would you ask for permission to write and run a script? If not (and presumably you wouldn't because that would be silly) then you shouldn't ask to run Emacs. You "own" both and take on all the "risk". There's really no difference.
But really, truly ask yourself, is whatever cause you're working towards (that is, the mission of the company) worth sacrificing your dignity for?
