"Doesn't that then immediately link an anonymous site to an entry in a global unchangeable ledger"
In a way, but three factors limit how bad that could be for them:
1. Wallets can be created easily, so in the worst case, it's linked to an empty wallet. Some Tor sites already accept donations through cryptocurrency, so known wallet IDs aren't that rare as it is.
2. There are some cryptocurrencies that are designed not to make public information about previous transactions, so they could use one of those.
3. It wouldn't be very hard to make a pool of a lot of different people, including but not limited to the hidden service. If you mined in the pool, you'd know that one of the twelve thousand wallet IDs in the pool belongs to the operator of the service, but not which one. The pool wouldn't have to know either; as far as they know, they get hashes from someone and pay out, but they don't know who did the hashing.
I'm still glad they didn't go that way. It would inevitably lead to more abuse and, by using a more complex system, there would be more capacity for vulnerabilities in a protocol that already has a few but to which no alternative at a similar scale really exists. Oh, and it would be more unpleasant for the users.