gave you a "thank post" for the nice reasoning post but that doesn't mean I like where this overall thought is going :p
Imho, good braincells wasted on trying to come up with the best way to fix something that merely exists "because they screwed up" - there is no way around that, period. Granted, the anime up to the last episodes is pretty decent, granted there surely were some production constraints that led to this mess, it's not like they raped the original story on purpose. Granted it is possible to see anime spawned by manga as a piece of art/entertainment in its own right - but if you do that than that would mean what's done is done and there is no purpose whatsoever in trying to fit it back in with a season2 following the manga. Saying it is a piece of art in its own right and deserves to be accepted as is and in the same breath saying well, now that we established that fact let's see how we can fit it back in is contradictory line of thought.
Guess what we have is probably the result of some executive in production insisting on "their" story getting closure at a point where it was already known that there would be no season2 fundings while the second half of episodes were still in production. So they made the best of it in terms of "their" version of the story and it is a decision you can take but I think there is room to assume it was a decision made not by people giving overly much attention to original storyline - rather somebody did the maths on what a finished story needs in terms of standard plot elements and said "oh well, we have a heroine, we have a main antagonist, that shit at the least has to get resolved than - as Clare craving revenge was her prime motivation we gotta get that in and resolve it ...also, this way we can get in green lasers into a fantasy style anime - I like green lasers you know...:cheez"
.... and so it was done.
Imho, best option would be a huge budget complete redo :mono - slightly more gory, yoma getting red blood not violet ... a bit more harsh as things are in the manga with the early fights and people dying by the score... also really staying true to original in every detail except for adding some slight amount of additional angles/shots of the fights to get them more dynamic and fluent overall than in first anime...
second best would be to redo Pieta in OVA style and after some 4 OVA eps that push the franchise announce season 2 that takes of after the ova eps/ after time skip ... (kind of like with darker than black where the 4 Ova eps bridge the missing content between s1 and s2)
third best would be redoing Pieta in an ova style full length90min MOVIE and then moving on
and fourth would be starting the story after timeskip and correcting mistakes in flashbacks, - also thinking of viewers here who do not know the manga, thus watch season1, and then wonder about the mess afterwards - the multiple flashbacks deviating from the first anime while simultaneously linking back to it would be more confusing to them than say a completely re-done Pieta arc
