The more I think about it, this could be rape-free AND abortion-free, though still tragic, and connecting a ton of things in the game.
Okay, so Mado does it with Masada. He has some kind of defect of his own, signified by his eyes (a HIGHLY recurring sight, you'll see it in places you didn't even realize if you look for it). She fears a deformed baby, though she doesn't know what exactly it'll look like. This could explain all kinds of images, from the wall drawings to Mars-san to The Thing With The Quivering Jaw and the Colossal Bleeding God (a name suggested for the thing in the sky after Uboa). Maybe even Monoko, though I still think the traffic accident is more likely for her.
Takoffusen is only one of the many, many deformities in this game, and I think it only represents one of countless imagined offspring. After all, chances are you'd never even see it before finishing the game.
Pervasive feelings of judgment/guilt still apply from the above theory (hence she won't go outside), as either Mado's considered too young to have a child, or that she was wrong to take advantage of someone like Masada who maybe wasn't right in the head.
The bloody zipper could symbolize the moment of the act, Kyukyu-kun is the happy fun time, and FACE is the deformed sonogram directly resulting from that, hence its closeness to those things.
If she was still pregnant at the end, that explains why there are two jellyfish and not one.