Not trying to make him look good. I am not the fan I used to be. Jefferson was way too much the fan boy of the French Revolution for my tastes. Just trying to be fair and not just pile on because it’s now fashionable.
Anyway, Jefferson was gone from Monticello through most of that time period. Even when he was there, I doubt he kept tabs on his brother. Another candidate is his brother’s son Isham Randolph Jefferson who was known to be there more often then Randolph.
There's no way that we'll know if it was Thomas. Only that it was one of the Jeffersons. Unless we're able to discover more evidence somehow. But it isn't too far-fetched that Thomas did it himself. Most people are flawed humans, after all.