It doesn't surprise me that they are doing this, but it surprises me that they aren't at least going the jetBlue route at first and doing something like 50% miles for flights through non-preferred agencies. There is going to be a lot of negative customer satisfaction for the next year with people who purchased through 3rd party agencies (say, a vacation package through CheapCaribbean) and had no idea their flight wouldn't earn miles.

They don't say, but I'm assuming that AA marketed flights won't earn miles with any FF program, but codeshares (e.g. BA 7832 LHR-CLT operated by AA) still will.

If I was a "non-preferred" agency, I would start flagging AA marketed flights on their site as "doesn't earn miles" in a way that is vague enough to make people think that it applies universally, guiding people to airlines where people can.