Every tool is also a weapon, obviously. We haven't stopped making hammers because they can be used to hit people.
It's like being afraid your browser profiler is being used to spy on you. Could it do that? Sure. but there are so many easier ways to accomplish the same task.
[EDIT] and, especially, that's why they're jumping to the conclusion that github is gearing up to do more spying on its users, which is the part that I think people are bothered by, not the existence of this software package.