I would propose to really start worrying once we:
a) know for sure the deal goes through. As far as I know that still hasn't been officially confirmed.
b) know for sure that the plans MS has with Minecraft are bad for us and the modding community. This is also far from certain. We simply don't know what MS plans to do. So it is useless to speculate about it.
I agree with this plan in part.
The deal is going through. However, FTB and other like communities no doubt should still form a two-part plan:
a) Wait to see if they let you keep modding or not;
b) if they let you, all is fine, do nothing. If they do not, form a development community to make a new game. You would be allowed to use any part of the FTB mod ideas you liked. Mojang does not own Buildcraft, for example. All of the ideas in that mod you would be rightfully allowed to use for a new game. Minecraft, on the other hand, would not, and would be breaching intellectual property rights if it does. Just don't use what Minecraft DOES use. By that I do not mean you can't have mining or farming etc; yes indeed you can. There are thousands of other games that do. Just vary it enough to be not a direct copy. And with all those ideas in FTB, it's already most of the way there.