I hear "the guys" meaning "my group of girls", said by a girl, often enough. But I agree that the guys has a somewhat less neutral connotation.

Interesting that your cohort is fine using "cohort mates"! In most contexts I've been in, people would tend to view anything nonstandard and with that many syllables as a stuffy, impersonal way to say things. But there are a lot of contexts I haven't been in.