I couldn't agree more: Twitter looked really petty and stupid. Fact is, it made a really bad choice in its first attempt to fact-check Trump. As you highlighted, Twitter chose to fact-check an opinion. But, by the basics of logic, that can't be done.
As I argued in another Medium piece, Trump's words are a conditional prediction about the future. His prediction cannot be fact- checked without a time machine.
The larger question is what to do about the threat media giants pose to free speech. I've argued the law needs to be changed so any sufficiently large social media network would have to provide a neutral platform option for its service. Twitter would be allowed to offer customers an option for a censored Twitter where they cannot see any of Trump's tweets. Or they could offer a version where any tweets not approved by Twitter would get a Twitter Fact Check box. I am not sure how many would sign up for any of the Twit versions of Twitter. But that would allow market forces to operate and prevent Twitter from exercising monopoly power to advance its own opinions. Trump's order may not be entirely within the bounds of current law, but he is moving in the right direction, towards greater fairness and freedom.