(I work at MIRI.)
News that SIAI received funds from Epstein actually came as a surprise to us. (We found out about this a few days before OP's question went up.) Epstein had previously approached us in 2016 looking for organizations to donate to, and we decided against pursuing the option; we didn't realize there was any previous interaction between MIRI/SIAI and Epstein or his foundations.
The 2009 donation was brought to our attention when someone sent us a Miami Herald article that included SIAI in a spreadsheet of organizations that received money from one of Epstein's foundations. We couldn't initially find evidence of the donation in our records, so we had to go digging a bit; it was apparently seed money for OpenCog while they were getting up and running rather than money for "real" SIAI stuff, hence current staff being out of the loop.
My bet would be "yes", because it doesn't seem to be a frequent name, and the set of people who can donate so much money is not that large. It could possibly be a relative with the same first name, if such person exists.
I also think it is irrelevant, but I am curious about the meta level: If an organization has to disclose the names of donors (not sure if SIAI has to or not), does it also have to provide answers to questions "is the XY who gave you money this specific XY or a namesake?"
Would it make sense for a group of rich people to coordinate and legally change their names to the same (already frequent) name, thus making their future donations deniable? Imagine that George Soros, Peter Thiel, and the Koch brothers would all change their names to "John Snow", and then many organizations would be like "yeah, John Snow donated tons of money to our cause, and we are not legally required to tell you which one". :D
There are plenty of ways to donate anonymously already when that's what people want to do that take a lot less effort then changing a name.
MIRI's website mentions a list of their donors. However, the list does not mention Jeffrey Epstein. I found that name on a list of donors from 2011. Perhaps, the scandal or conviction of Jeffrey Epstein made MIRI remove his name.
Is the Jeffrey Epstein who donated 50000 dollar to SIAI, the same as the present famous one.
Ps. I think that this question is irrelavent to the normal environment of our forum, but I could not control my curiosity.