One can only hope there'll be a watershed moment like the one that killed Digg. So far, reddit has been very careful raising the temperature so as to not scare the frog before it's dead.
That's maybe true as a first-order effect.
But, for the ads that everyone else sees to be worth anything, the site has to be worth visiting at all. If your most dedicated/prolific users mainly post/comment using third party apps, then making their experience worse will reduce the quality of the site overall (even if you start getting revenue on behalf of those dedicated users).
It strikes me as a very shortsighted move.