I gotta figure it's more about the fact that if he can't start serving a suspension until he's signed, it's going to be harder for him to get a deal. What team is going to give a guy a contract and then be forced to let him sit for 41 games but still pay him?
It's all mostly explained in the article. Sounds like the investigation started during contract negotiations and Ottawa and Pinto stopped negotiations. Whatever the violation was it wasn't gambling on NHL games, but it's severe enough that Pinto was appreciative of how Ottawa has kept it under wraps so it sounds like a rather personal matter.
Speculation on my part; the NHLs hands are kind of tied. How do you assess a cap penalty for a player with no cap hit? He's an RFA so Ottawa really doesn't need to do anything with him, and can maintain his rights, as it's basically like a player leaving for Europe. The other examples brought up all had a tangible dollar figure that could be applied as a penalty. But the league doesn't really have anything they can do in this instance.
The CBA only allows the league to fine a player, void or cancel the contract, or suspend the player. So honestly this is about all they can due since their is no contract to void and so no set amount to apply as a cap penalty.