Does the same reasoning apply to all -isms? Empircism, materialism, internalism and externalism to name a few.

ism has a few different uses it can indicate a group of principles (empiricism), or a political movement (socialism), or a type of discrimination (sexism).

Your worry seems to be that "rationalism" looks like a political movement, but that sort of thing is more likely to be determined by how the people who use the term of themselves act. And that problem does not go away by refusing to use certain words. If people who call themselves rationalist try to spread their ideas through exerting political force rather than calm argumentation then it is going to look like a political movement, whether or not a ism is being used.

If you're worried about this then you need to deal with the underlying problems, not just worry about words (after all, I'm not aware that empiricists have this concern).

As an aside, I think the main reason for not using it is that it already taken: http://plato.stanford.edu/entries/rationalism-empiricism/