Accepting btc was probably more because of convenience of payments etc instead of anonymity.
Had it just been this one Apple purchase or a Facebook visit then I'd agree, there's always something you'll miss and it's much easier to point this out afterwards. But it appears that he didn't use a single method to hide his identity.
On the other hand, perhaps he thought that living in the Ukraine would give him enough protection against US agents.
The hindsight bias is realizing how serious the situation might be and the level of OPSEC that is required. When the torrent site was first created the risk level wasn't known and most people didn't understand how hard it is to avoid the ubiquitous sensors of the surveillance-industriual-complex. Yes, more people probably should have assumed this level of risk much earlier, but that's easy to say now when we know names like Prism and XKEYSCORE.
[1] (note: contains rude/strong language) https://www.youtube.com/watch?v=J1q4Ir2J8P8
The proof they collected by connecting the IP to Facebook is a bit more advanced (although not complicated if you have a court order), but it appears that he didn't take any measures to hide his identity.
I thought that using a (non-US based) VPN and fake data for domains is the least you'd do if you run a website that could cause trouble. And accepting bitcoins is nice but not anonymous if you register the wallet with the apple ID that you use everywhere else as well..