The most significant thing about this, is the fact that we have absolutely no idea what they will do. We don't even past examples of companies doing the same thing, because this has not, (to my limited knowledge anyway) happened before. Most companies don't buy their secondary markets. It's simply not done.
Now, this is just my logical conclusions on the situation, and should not be taken as fact, or conclusive by any means.
The main reason most companies don't do this, I believe, is due to one main factor. And that is the lack of competition provided by these secondary markets. In most cases, the aftermarket is for older, second-hand, and third-party products. The competition simply isn't there. If anything, it can be selling point for some, like, "hey look! Look at all these cool extras I can get for that gizmo if I buy it!" But in the end, the company doesn't lose much money.
With Lego, it's a different story. Lego's product, has remained unchanged for several years. In addition, their products are of fantastic quality, with no amount of disconnection from previous versions of the product. Buying peices second-hand, can be often be much cheaper, than buying a new set for the same parts. Thus, lego doesn't get that sale. So, the secondary market becomes competition at this point. And what do companies do to get rid of competition? Buy, or force out the opponent. That way, they make the money they would otherwise loose to the secondary market.
Currently, I think it's in Lego's best interests to keep BL the way it is, for both PR and logistical reasons, but I certainly believe there will be changes, if merely a streamlining of the process.
But, I don't know, this is purely speculation on my part.