OH MY GOD THANK YOU!!!! as the writer i was waiting for the day someone would try to dissect my 4 am yap lines HAHA. yes ellie is stupid. she is so so naive and i tried to make both characters super hypocritical (the game is supposed to make you think about your own hypocrisy regarding world issues)!! yes they are basically sapphic hehehe and like the lines you noticed (THANK YOU FOR NOTICING THEM i've been dropping hints and revealing it in the comments) she is used to not being so close to coworkers (to answer your question on why miss kills ellie, it's bc she thinks of ellie as a "failed experiment" and is used to just disposing of them like that), but she felt some sort of attraction/pull towards ellie so she's really depressed about it.
miss's hypocrisy is knowing she's not really doing anything for the world but doing all this anyways (she even hurts innocent ppl like ellie) + the timeline thing you noticed :). ellie's hypocrisy is still the "No one should go through this. Except you." line bc she is super adamant that no one deserves to die even with that dead guy committing so much harm (arguably way worse than what miss's killing), yet she doesn't apply it to herself when she's at the other end of the knife. of course it's normal for people to think like that -- it's so normal for people to speak like they're heroes then turn around and act in a way that shows they're not. this was an allude to "pro-life" supporters who get abortions (or don't support policies that would support peoples' lives after birth) or anti-lgbt politicians who lead an lgbt life under the table (have you seen the sharp rise in grindr usage during republican conventions? it's rly funny).
and LMAOOO is the best ending really just the speedrun ending?? 😭 it could be argued that it's not though bc ellie would've kept living in naivety
also i wrote an essay abt mimco (cited it as an indie game... my prof doesn't know i wrote it 🤭) and this comment reminded me of that HAHA