Time will tell; you may be right. But I think some people (myself among them) view this as a dominos situation, with one falling after another in succession. I think without the cover of the conferences and CLC, the individual schools may be more exposed in a legal sense to future similar litigation (which I would guess is what all of these pre-emptive moves are about).
It's true that not having to shell out for a license saves EA money in a direct sense, but if the number of people that don't buy the game because there is no "SEC" (no SEC title game, branding, etc.) results in a loss of revenue greater than the upfront fixed cost of securing the license, it will be a net loss for EA. My guess is that there are a lot of people that won't buy the game if there is no "SEC" in it, since most purchasers of the game are casual gamers, not hardcore, and just want to take Alabama or LSU to the SEC title game.
I think it's easy to envision individual schools, i.e. Notre Dame, taking a similar prophylactic tack as the conferences and reducing their exposure to future litigation. I would imagine that the logic of the SEC and B1G pulling out of their EA deals is the same calculus as exists for the individual schools. I don't know what's going to happen, and I don't know the law or the case well enough to say with any confidence, but it seems to me that it's only a matter of time before schools start bailing.