I doubt that. You see, RUF is recognized, by government regulations, as a separate car brand from Porsche, as the only thing they really take from Porsche is the chassis and some of the bodywork, and they have no official ties with Porsche.
As for Alpina, they have extremely close ties with BMW. Their cars are sold, through BMW dealerships, as "BMW Alpina" models, with a lot of the assembly occurring right on BMW's production lines. Unlike RUF, a lot of the parts are BMW-sourced too, including major drivetrain components, most of the bodywork, the interior, and the chassis. Because of these ties, Alpina models have to be approved by BMW before being put on the market. Most importantly however, the cars still feature BMW badges, the rights to which belong to BMW of course. Strictly speaking, it could be done with a couple of workarounds, but I don't see BMW liking the decision too much, and Alpina certainly wouldn't want to hurt their relations with them.
It's not that I don't want BMWs in the game, I'd love to see them, as well as Porsches and Lamborghinis. But I'm almost certain it won't happen, not in TDU2 at least. However, perhaps EA's exclusive license will expire by the time the game's successor comes around (If there is one in the works).