The Trump admin was very creative when it came to Harvard and figured out many different pressure points to push all at once. Don't expect it to be too simple. The guys running this have thought about avoiding the easy dismissal: https://www.ortecfinance.com/en/about-ortec-finance/news-and...
Just look at how the recent flag burning EO was worded in order to get around 1A concerns.
The Wikimedia Foundation does not depend on US government funding and even if the US somehow made life difficult for donors, they are sitting on a substantial endowment fund that can float them for a long time.
And at some point, if the harassment gets to be too much, Wikimedia can just up and leave. There's no reason that the Wikimedia Foundation needs to be headquartered in San Francisco, it could just as easily be in Oslo or Paris. That's a huge advantage that Harvard didn't have.