By not stopping it, Hinch "condoned it." He's the manager, and he knew it was going on.
What the Sox have done or not done is still be investigated. So far, we only have allegations.
It does not look good, but we don't know exactly (proven) what the Sox did. Like the Astros, I doubt the higher ups would know, or they shielded themselves sufficiently, as they nearly always do.
The second offense does carry a lot of weight, but it also depends on how much they can prove and just how bad it was.
If, for example, it's way lessof an infraction than the Astros situation was, does the fact that it was a second offense make the punishment similar? There's a lot that is hard to know, right now, but things look real bad for Cora. The Sox situation is still up in the air, but it looks like it's heading for a crash.