Here's what I like to think, me and my ignorant self. Why name something after a word? Most folks would do it because they think that whatever meanings and connotations that word already carries would apply well to the concept being named. I see your quoted Grothendieck as a strict practitioner, and indeed a master, of this style of naming: think of "etale", "crystalline", "topos"...
However, this point of view ignores an important aspect of the naming process -- its bidirectionality. Once you name something after a word, the word is forevermore changed in its meanings, connotations, usage, and cultural presence, by simple virtue of being attached to this thing it wasn't attached to before. That is, it's possible to view the act of naming not as applying a word to an object, but applying an object to a word.
Coming to perverse sheaves, the question was why such "beautiful" and "well-behaved" objects deserved the name perverse. Certainly from Grothendieck's perspective on naming this seems to be a travesty; but from the second perspective it makes perfect sense: how better to soften the harsh and pejorative word "perverse", at least in certain (mathematical) circles, than to apply it to such fantastic objects?
I view the naming of perverse sheaves as a brilliant and subversive act.