Will there be consequences for not participating in ShutDownSTEM?
Will our disobedience lead to trouble later?

Anything is possible, and some things are a lot more possible these days than they were just a couple of months ago. It’s quite reasonable for you to be worried.
But let’s be clear. You didn’t “think it was a joke”. That is a poor way to explain your outlook and increases the chance that you will be criticized, perhaps harshly, by people who don’t have patience for nuance, facts, and the intricacies of human nature in these turbulent times. It’s probably more accurate and more productive to say that the whole thing was so unexpected and took you so much by surprise that you did not immediately appreciate how important the shutdownstem event was as a way of expressing your support for an important social movement. Thrown off, unsure what to do, and being a creature of habit and passionate about your work and its importance to science and to society, you ended up sticking with your usual routine. ... Right?
Similarly, I think it’s a mistake to use the word “disobedience” to frame your behavior. Researchers in US academia do not take orders from anyone about when or with whom to hold meetings. If you carefully read the emails you received I am sure you will discover that none of the stuff about canceling meetings and participating in the shutdown day is phrased as a directive. It was almost certainly a “suggestion” or “strong recommendation”, or you were “encouraged to participate”, “invited to reflect on systemic racism”, etc. And indeed I am confident that you reflected on many important issues that day (and most other days in the last couple of months), as pretty much everyone has been doing. Do not play into the hands of overzealous activists who presume to see into your heart and know what you care about and what you don’t care about by professing to a willful disobedience you are not guilty of. Instead, anyone criticizing you for not participating should be forced to acknowledge that the invitation to participate was precisely that - an invitation, making it entirely reasonable and acceptable to decline.
I could go on with a few similar things in your post that suggest a somewhat cavalier attitude that opens you up to a heightened level of scrutiny and criticism. Please try not to give anyone asking about the shutdown the impression that you find the recent nationwide events uninteresting, unimportant, or not worthy of being thought about or taken seriously. When you write things like “I purposely isolated myself from real-world news”, “reflect on ... something”, and “send them on their way” you sound dismissive and create a serious risk of being misunderstood. Since you support the cause of the activists, it would be foolish of them to come after you, but if by your words you give them the wrong impression, it’s quite possible that some of them will not be as thoughtful or charitable to you as they should be.
Bottom line: think defensively about this. Your actions were reasonable, but much could depend on the precise way in which you explain what happened if questioned. Also, find allies who know you and would be willing to come to your defense if push comes to shove. I hope it doesn’t come to that though, and it very well might not. Good luck!

Edit: note that I am posting here using my real identity. In such times when discussing potentially controversial topics I’m always cognizant of the possibility that in the process of offering advice to some anonymous person I never met I may be inadvertently opening myself up for potential attack or criticism by anyone who disagrees with what I wrote or interprets what I wrote in a different way than how I intended.
Oh well, it is what it is I guess. But just to clarify in case anyone gets the wrong idea about what I’m saying: in this answer I’m addressing OP’s concern about possible criticism and/or career damage given their actions during the recent STEM shutdown day of protest, and only that. I’m not commenting on any political movements or points of view and their significance, worthiness, virtue etc, so please do not interpret any of what I wrote as commentary of that type.