Of course, someone could argue (analogously to this article) that the problem with the phrase is that the members of the People's Temple in Jonestown didn't drink poisoned Kool-Aid as often thought, but rather a different product called Flavor-Aid.
When I was working for a large US tech company, one of colleagues used that term to their American managers in a positive way (we were Linux people, after all): turned out he didn't know the origin. Significant faux pas!
I hear this used all the time with various meanings ranging from "being fully committed" to "being brainwashed". It usually implies a naive level of (or just misplaced) zeal but I feel like folks rarely mean the suicidal/homicidal part which can make the phrase quite shocking if you actually think about what is being said. Language and culture are weird.