Sometimes, need-of-the-plot considerations are more important.
I mean, take my Kotori for example.
Kotori got promoted to E3 just because her replacement-CO liked her face and thought she showed decent professionalism.
Kotori got a big promotion leap from E3 to O2 because her CO (Rufus) found her competent and wanted her to keep assisting him after her first mission on the Sakura.
Then, from O2 to O3, just because Yui agreed with Rufus that she showed promise.
And a bit later to O6, just because Kotori asked Yui permission to overrule the chain of command of another fleet and make sure she was calling the shots (the Battle of Tsuyosa). Yui decided it was easier to promote Kotori than give her a special command authorisation/battlefield promotion.
Promotions should never really go this way. I certainly don't do them like that in my plot. But at the time, Wes felt he needed 'good players' (I quote) to be in positions where they could make the most out of their potential. Heck, Wes still makes the occasional plea to have me allow him to make Kotori a Taisho. =P
I think it's a similar deal here. Here, a metagame need needs to be filled. If it's filled, SARP is enriched by a new plotline. Therefore why Hanako seemed to take it in stride - believe me... Hanako could've been a
lot more annoyed.
So, I suggest you don't worry about it and just forge on. It's a little more inconsistent, yes, but then again SARP is a game and whatis the most fun is what usually works.