I got the impression (from reading the synopsis) that they were so annoyingly difficult to control that the Chairman just gave up and let them have it their way.
I kind of got the idea that having actually proved they could do something positive with free will, God gave them a new slate as a "you passed the test" sort of reward. I say this because Thompson says earlier on that they already tried twice to leave humans with free will, which indicates that the ultimate end game is for human beings to be able to procure their own future. Hence, David and Elise having proved that they can do that in their one individual example, God gave them the opportunity that the human race as a whole hadn't proven itself ready for. This was pretty much stated at the end, anyway.
It wasn't a Deus Ex Machina. The movie made it clear by the end that humans have to earn their own free will. They have to want something enough that they'll give up everything for it, and will deviate from the plan (whether they know about it or not). David and Elise were so important to each other that they absolutely refused to give up, despite the fact that staying together could mean that David never becomes the President and Elise never gets her fame (Elise didn't know this, however, but she did choose David over the man she was about to marry, who seemed a whole lot more stable than David did at the time). They had proved that they could handle free will and had passed the Chairman's test. If you didn't like the movie, that's perfectly acceptable, but it wasn't a Deus Ex Machina.
It's fitting with the Bureau's representation as a bureaucracy though. The Chairman (who HADN'T been absent, he was mentioned dozens of times, each Chekhov's Guns) is perfectly capable of writing a new plan—he does it all the time. He's just impossible to get to, because otherwise he'd be inundated with requests, and would get nothing done at all, just like the real head of a bureaucracy. The situation simply became a large enough debacle to finally reach his attention, and it was unjust enough that he felt he should rectify it. It technically is Deus Ex Machina, true, but far from coming out of nowhere, I actually found it somewhat predictable.
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Kept its head above water until the last scene
The film was watchable, and even had a few parts that were legitimately entertaining. The characters, while not particularly thrilling, were more interesting and relatable than typical Hollywood fare and had a modicrum of depth. The buildup to the finale had the momentum and interesting plot devices that should have been present throughout the movie, and the final chase scene was enjoyable.
Unfortunately, the ending is a hairpin Deus Ex Machina. I mean, the protagonists are literally backed into a hopeless scenario due to their own choices and the very nature of their situation, then God (who had been completely absent until that instant) shows up and fixes everything for no adequately-explored reason. The ultimate fate of the protagonists beyond the fact that they can now live out their lives goes unrevealed- they solved the immediate crisis, now go home.
In short, this film had much more potential than it managed to act upon. Watch it if you just like fancy hats, otherwise just go watch Inception. In fact, either way, just go watch Inception.