Tbh the sentence doesn't make a lot of sense - it reads like somebody tried to incorporate many advanced vocabularies without really understanding how they are used. There are also a few grammatical mistakes.
Having said that, if I'm forced my guess would be that the opponent kept his gaze on the attacker, despite (other parts of the body) being punched away.
It's very hard to tell though, as 瞳 is overwhelmingly used for adorable things. An exception is when it's used to describe the pupil specifically, so it's possible but it's not obvious to me why the writer would focus on the pupil. It's also a physically odd situation (body moving away but the pupil remains?). ぶっ飛ぶ can also refer to blackouts, but then it's also odd (one is unconscious, but the pupil remains conscious?).
I think you'll have to ask the writer - maybe they knew what they wanted to express, but they are probably not yet proficient enough in Japanese to express it.
EDIT: After looking at the context, I suppose the writer is going for a VERY creative, unorthodox writing. They probably added the "め" in ふりがな because hitomi wouldn't fit (it will make things sound very adorable), but they still wanted to focus on the pupil. They also say "拳が潤う" which is extremely odd （潤う only refers to pleasant moisture), but it makes sense because the character then talks about erection... "潤わなかったなんてねーのに" is probably a misprint of "潤わなかったことなんてねーのに". I think you have to interpret it with your own creativity. It's not a common expression by any means and I guess you are meant to interpret it in your own way.
甘ちゃんクセに-- 「甘ちゃんのくせに」？