So what if the subtext for Season 2 and/or Season 3 involve Section 31, horrified at the damage caused by the Klingons, decide that the Federation needs to radically change in order to survive and make sure this sort of thing never happens again? That they blame the logic extremists -- if not Vulcans in general -- for undermining the war effort and believe they must be purged from the Federation or dominated entirely?
You make a good point about the potential for timely commentary. But the downside of doing a prequel is that we know the outcome. The Federation doesn't change its philosophy, or purge the Vulcans, or do anything similarly dramatic, so we would end up going through the motions to reach the inevitable Star Trek Moral Conclusion. That's how we got the heavy-handed sermonizing at the end of the first season. When the message is obvious from the beginning, it starts to feel like a lecture.
To me, the potential for doing that sort of storyline well on Discovery is much more at the individual character level. They had the opportunity with Lorca but threw it away.