While I think the standard, generally-accepted definition of "Mary Sue" has moved beyond its original narrow remit and certainly beyond the realm of fanfiction (to a point where, arguably, it has lost a lot of its meaning) I'm prepared to accept that, semantically at least, O-Chul here doesn't fit the mould. So can we leave that point behind and focus on the substance of the criticism rather than the labelling?
Yes, Superman is an iconic character and has few if any character flaws. But there are also a lot of really terrible, boring, Superman stories: the guy hasn't been done successfully in cinema since the 70s - and not every flawless character is as iconic as Superman. Indeed he's probably the exception there, rather than the rule, and not a particularly stable exception at that.
So while flawless characters are not necessarily bad, they nevertheless I think need to be handled carefully, and that what is a tricky area to navigate has been done successfully on occasion before doesn't mean it automatically gets a pass.
I'm not saying I didn't enjoy the story overall (although I do think it's my least favourite of the backer stories so far). But I did have some problems with the characterisation in particular.