Connotations don't study history or philosophy, what matters in the context of Drexler's article is prevalence in popular perception, and resulting normative recommendation.
I don't see any evidence that the specific practice of naming scientific theories by the names of their founders, with or without the -ism suffix, actually has the effect that Drexler complains about, let alone that this effect is of such magnitude and importance that it would justify describing it as "pernicious." Do you?
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".)