Not only does it not seem to be a free speech issue to me, from my point of view this is basically the best-case scenario for avoiding censorship of contentious issues on dominant platforms like Facebook/Twitter. It's the obvious conclusion to arguments like, "the way to deal with bad speech is with more good speech."
Twitter saw speech they disagreed with, and they fixed it with more speech. They haven't censored any of Trump's arguments, they didn't delete his tweets. They just added their own commentary on top of them. That's what Republicans have always claimed they wanted. Argue that people are wrong, don't censor them. Don't throw people off the platform, add a fact-check.
I grew up listening to Republicans rail against the Fairness Doctrine, and I basically agreed with them on that point. Forcing private broadcasters to act like they were neutral on every issue was problematic. But now apparently that's flipped and free speech means forcing a private company not to take sides on any issue, even when taking a side doesn't require censoring or restricting anyone else's speech.
Any Republican that was genuinely anti-censorship would be cheering Twitter's move, even if they disagreed with the content of this particular fact-check.