Languages and words evolve. We aren't talking about Shakespeare here, it's a term invented by the Internet originally used to describe self-insert female character in fanfiction. It's been a while since the Internet has started to use Mary Sue to describe also overly-perfect, wish-fulfillment female characters. You can either accept this change or start bickering every time with 85.74% of the Internet about this change.
Erm, but that's exactly what the term means. It is a "self-insert" as a wish fulfillment. The male version of a Mary Sue is a Gary Stu. Chitanda doesn't remotely apply to this description because she is a character with annoying traits and is always placed in poor social scenarios. She might be otaku-bait, but that isn't remotely close to being a Mary Sue. No one -wants- to be Chitanda.