I'm not convinced. I don't see why the video game company has any reasonable claim to the footage in the first place (I'd argue that the video game footage is "transformative", not "derivative"), and I'm not convinced that its use in a Let's Play isn't, itself, fair use.
To be clear: I'm not a lawyer, I'm not advocating people go back out and re-enable monetization, but I'm certainly not disabling it, as I don't buy the underlying argument, and I don't buy that Google is intentionally screwing people over by offering them monetization rights when they know perfectly well that the content cannot be monetized. I WILL, however, advocate you do no more than turn off monetization on a video in particular, not for your entire account. If you don't think you have monetization rights for a video, don't demonetize your entire account, just don't monetize that video. If you don't think you have the right to post the video, I'd recommend against posting it at ALL (unless you're engaged in some weird, civil-disobedience centered cyber protest. In which case I'd recommend you maybe rethink your medium?)