The way I see it is, within the continuity, yes they're saying this is the first class. However, should they do a sequel to this all they'd have to say is that the fallout from these events caused Xavier start a new school with Cyclops, Jean, Beast (slightly older), and Storm. The movies don't have to follow direct comic continuity but at least they can steer it into an amicable (for the butthurt uber fans) direction.