It seems that it is pretty much confirmed that was the btc-e operator, and I have read no reliable reports about that being related to bitmixer.

Interestingly enough, the indictment was filed under seal on June 21, and bitmixer was announced to be shutting down two days later. It makes me wonder if either bitmixer was either somehow involved (meaning they were being run by the US Government), or if they had advance knowledge about the indictment (meaning they received requests for information from the US government, and were potentially provided information about their service they did not like).

Thinking about it a little bit, I think it is more likely to be the latter. Blockchain analytics companies have the ability to trace (larger) amounts of bitcoin that flow through most mixers, and it is possible that, as part of a request for information from law enforcement, they were provided with certain stats about their service regarding how much flows through their service from things like DNMs and ransomeware.

A little bit less likely, but it is also possible that bitmixer was in fact part of this. The indictment has a couple of paragraphs redacted, one of which is regarding a related company to the Alex guy. I suspect that some of btc-e servers were seized by law enforcement, causing them to go offline, and it is possible that some of bitmixer's servers were also seized.