Why do you think they're rebelling? Isn't the most natural interpretation that the corporate statement ("we don't want to profit from this issue") is accurate, and that Conde Nast doesn't mind if Reddit runs the ads?
I would say no, so it seems that the reason that the ads are running for free is because of the difference in opinion with the parent company. That's how I reasoned out "rebelling", although it's obviously a bit of hyperbole.