I don't know why every other thread around here turns into a discussion about FLE or Harry Potter, but here goes:
Honestly, I'm not too sure that Disney is overly concerned about WWoHP. I can't imagine anyone going down to Florida from too far away and visiting only Universal. Considering that the prices are about the same, and that Universal is done in three days or so, it could mean that they actually end up spending a few days at WDW that they otherwise wouldn't have spent. People who are closer to the Orlando area might be more inclined to make a trip to Universal over WDW, but that's not really Disney's focus.
Even if it is cutting into profits, there's a good chance that the fad wears off pretty quickly, and everything will be moving normally within a few months. Perhaps Star Tours 2 is part of Disney's plan to bring fans of a franchise back to WDW, and if it's based off of the original trilogy, it might do an okay job of getting back those profits. I can't see Star Tours taking on all of the losses for a larger franchise, but there's a possibility that it makes up for a piece of it. Maybe we'll see some more exclusive merchandise over at Star Tours' gift shop to get some merchandise sales that attempt to rival Harry Potter's.
As for FLE, it's not in any way directed at WWoHP. To me, it seems like this may be a fair response as far as merchandise sales go, considering that these are two large franchises, but it in no way is taking any attention away from WWoHP. In fact, it will be three years before it's complete, and by then, I think the WWoHP fad will wear out.