I think the concern is that it will now be used as a Deus Ex Machina in the future, not that the single event is one. So when Chuck is in trouble in season 3 he could pull anything out of the intersect. Chuck is surrounded by elite enemy agents... Chuck turns into superspy and defeats them all with his bare hands.
Before, Chuck would have to bluff them out or come up with some crazy scheme. Obviosly they left things vague enough they can do anything they want, but my guess is that they will need to immediately retcon this a bit. That is, first ep of season 3 Chuck tries the Kung Fu thing again and it fails. Still, it means whenever Chuck is really in trouble he could be as powerful as the story needs him to be.
But this ending has two clear and opposite readings. As it season finale it is as you describe. But as a series finale you could read it in a much more final way.
John jumping forward is how he survives Judgment day and Skynet hunting him -- this is how it happened. That is, this is the original timeline: this is how John met and befriended Derek and Reese, John Henry is how John begins winning against SkyNet and reprogramming Terminators (his secret weapon). So eventually he must send Reese and Derek back, he knows Allyson will be killed and replaced by Cameron, etc. He had to let his mother go, and she had to let him go, to move forward save everyone else. He has to be with this people knowing they he will send them to their deaths because this is what has to be done.
In this reading, the reason why future Jon trusted Cameron unconditionally is because he knows her future -- he knows she'll sacrifice herself to save John Henry.
It's a neat trick of writing that the same ending can be open enough to serve both purposes while still managing to be satisfying if it indeed the last word.