It's subversive because you think it's the typical "sometimes you have to do bad things to stop worse things from happening" plot.
But nope, committing atrocities because that's the standard of the "bad guys" is what allows terrorists to justify their existence and propagate the cycle of violence. The entire plot of the game is that individuals in the US and Russian governments use terrorism to justify even worse actions.
The game mentioned in the OP, on the other hand, portrays Palestinian liberation as requiring violence in order to match the actions of the Israeli military. The killings are not only justified but are necessary. This follows Frantz Fanon, who said:
> At the level of individuals, violence is a cleansing force. It frees the native from his inferiority complex and from his despair and inaction; it makes him fearless and restores his self-respect.
In other words, getting revenge is inherently cathartic and the solution to a violent conflict is to ensure your side performs more violence and ultimately wins. It's a very different message to Call of Duty.