Of course, even if we presume that naming ideologies as "isms" causes a bad reaction but naming scientific theories doesn't, then I suspect that a randomly chosen outsider is at least as likely to put the LW usage into the "ideology" camp as he is to put it in the "scientific theory" camp.
I feel that the term "rationalism", as opposed to "rationality", or "study of rationality", has undesirable connotations. My concerns are presented well by Eric Drexler in the article For Darwin’s sake, reject "Darwin-ism" (and other pernicious terms):
So, my suggestion is to use "rationality" consistently and to avoid using "rationalism". Via similarity to "scientist" and "physicist", "rationalist" doesn't seem to have the same problem. Discuss.
(Typical usage on Less Wrong is this way already, 3720 Google results for "rationality" and 1210 for "rationalist", against 251 for "rationalism". I've made this post as a reference for when someone uses "rationalism".)