Oooooooooh, this is quite an impressive theory.
But! As much as it makes sense, it's also possible that things may not go this way. I believe there was a rumour about a character reset around the time before MoF was released, but it didn't occur, even if it made a lot of sense (someone confirm or prove this wrong). It's possible and might be interesting to see where things'll go if ZUN somehow kill off Marisa but quite frankly I don't see this happening, because:
1- That would be an earthquake-like change in the setup! I don't think ZUN'll trade one of his character, even if she is genuinely irrelevant to gensokyo in-universe, for drama's sake. The way the storiES go are usually "Stuff happens, solving happens, go back to business as usual happens + something new in gensokyo" and reflect daily life in Gensokyo : it's hard to imagine how drama (cuz death=drama. ALWAYS) would fit in Touhou official works.
2- Marisa'll be needed for mechanism's sake! Touhou 15 is not in the works yet, but we can agree that it'll be a shmup game, just like the otheres main game are:
To me, Marisa (at least in the shooters) represents the classic "forward-focused max-power type". Therefore, I find it hard to believe that ZUN would remove her from the game. Her shot type is such a staple in games of the genre that he'd probably have to think of a replacement character in the event that she actually does leave, and at that point I think it would either be an existing character or a new one altogether. But knowing ZUN for who he is, a grand surprise is never out of the question. Heck, maybe Rin Satsuki will be introduced and replace her.
I guess this makes sense, but bringing a Marisa-like character out of the blue is unlikely
3- (This reason is more like an opinion) The games use spell cards rules. So, if he wanted to kill off a major character, it should be in a brand new literary work or something like that... and no such thing has yet been announced
4-
Japanese fans'll burn his house It'll be a huge fan disservice if that's what he gives for Touhou's 20th anniversary
5- Komachi's line leave a wide margin for interpretation, I guess? It's not like Komachi expressly said that Marisa'll die ten years later
How things'll end up comes down to what ZUN's gonna do and since there's already ULiL in the works, I'm expecting something along the lines of Touhou 14.8 (or 14.7?) to come next and, being busy dealing with the scenarios for Ibarakasen, Suzunaan, real life issues, the PS4 thingy and raising ZUNior, I do not quite believe ZUN might have the time to cook a big story that'll cause the death of such an iconic character.
Then again, we are only doing speculations. We are only in January 2015 so, who knows how things'll turn out? In any case, I hope your prophecy won't happen cuz I like Marisa (no offense

).
btw, about the way time flow, If PoFV, who came out at 2005 is more or less a consequence of WWII, 60 years earlier, then I guess Gensokyo's time flow the same way ours do.