The only pity is that Chiaki absolutely suits the intriguing story: poor child being in danger and noone can really help her (you know the rest). I don't think this line needs any lewdity. Even if we don't mention the main obvious reason, this will just not suit the story (well, includingly because of the main reason).
The new one Chiaki won't suit the story that well (a little child under threat thing penetrates right to the heart), so it will be felt differently, but the author will do his best, for sure. Also, new Chiaki is very cute and (contrary to the current one) naturally attractive in *that* way. Which is... well, natural and non-controversial.
Also, there should be no talking about two parallel versions. It will take not even twice as much of time to develop that, but a whole eternity (at least, I see it so, imagining the production process). Unfortunately, but for the sake of developement, we should just enjoy 0.4.9 version story with little Chiaki (or just keep it in our memories) and continue with a new one, with an adult (mature?) one. As a bonus, we will possibly have a new lewdable character (woo-hoo), which is an absolute cutie.
That "twin sister" thing reminds me of "Yosuga no Sora" with whiteheaded twins (at least they loved each other, unlike Minato and Chiaki).
Cheers, love, peace! <3