Here's the way it came down as I understand it: the only "punishment" handed out was a one month suspension of the GM. That's not punishing the team, it's punishing the manager, and it does nothing to undo the wrong perpetrated on the Red Sox.
What the Sox did in the International signings was what teams have been doing for years - they signed the players to a 'wink-wink' agreement for certain amounts of money, then gave the total amount of the signings to an 'agent' who distributed the money differently, giving more than was allowed to the higher rated players. They "laundered" the money through the agent.
No doubt that if they knew about it before the money was distributed - and I believe they did - it was unscrupulous, but it's been a common practice.
I agree that it was done to make an example of 'someone', but it sticks in my craw that they chose to make an example of the Sox in that situation and essentially let the Padres go free in another equally unscrupulous situation that involved Boston.