I can't imagine getting rid of the two most popular characters at the household, but fortunately the Dev gives us choices. Your way and my way are both still valid options at this point, thank goodness. Now, if you mean these things happen at the very end of the game (i.e. an epilogue), then I can get on board with that, but if it happens prior to the climactic third act, then no.
First, regarding Ain. Some players may enjoy Ain leaving the household, but for me I keep thinking, why in the world would I want to see (or worse, be forced to play as) Ain leaving to go be a sex slave/housewife to someone else? There are plenty of games out there that have the player take the role of a female character who just gets molested and fucked all game long. Desert Stalker is not that game. You're an alpha in this game, not a beta. And even if she is treated well by a husband, what are we left with? Housewife simulator? Borrrrring.
As for Shani, her becoming a Desert Stalker and having her own adventures might be the final goal, but now you're talking about a completely different type of game. Shani would be more of a Black Widow type character (the comic book not the shitty movie).
Shani is more well suited to using guile, deception, her sex appeal, and then finally violence when necessary. There is nothing wrong with that, but again that is not the type of game DS was marketed as. That would be a great sequel game or completely new game. But a 180 degree tone switch is not the way to go here. Finish this one with Zaton and then make that "Black Widow" game if you want a dedicated Shani protag or make a "girl walks around town and gets molested" game, with Ain protag. Story progression is one thing, but switching to a completely different tone and character midway is another.