If "Viola" was actually the witch the whole time, wouldn't she know her own house well enough to navigate through it easily, even with the puzzles set up?
Try navigating your own house when someone has rigged it with a billion death traps.
The house changes its configuration according to the controller's whims. With the Witch's body comes her magic, which Viola turns against Ellen.
According to the third pseudo-ending, Ellen gouged her own eyes out and sawed off her own legs "before Viola came to her house". I know Viola's a really nice person, but even then I find it hard to imagine she'd be willing to swap bodies with someone in such a state without even asking what the heck happened...
It was supposed to be for one day, which probably helped Viola decide to go through with it to give her "friend" a day of hapiness.
I'm guessing Ellen found some way to hide her condition; maybe she covered her legs with a blanket and wore a hood or sunglasses, so that Viola wouldn't see what she'd done to herself.
Confirmed in the side-story, The Diary of Ellen. She covered her eyes with bandages and her legs with a blanket.
How does Viola chase Ellen out of the house when she can't see? As in, she both can't see where she's going, and can't see where Ellen's going.
Either really good hearing or using magic and/or the house itself to track her.
Seriously, how long is Ellen going to be able to fool Viola's father? She has some of Viola's memories, so she may be able to impersonate her for a time, but given that their personalities are polar opposites and Ellen can't seem to resist her cruel and violent nature, I doubt it would be long before Viola's father realized something was very wrong.
Somehow I ended up with the interpretation that the Witch's House was an allegory for puberty. Probably overthinking it though.
At the end of the day, probably not for very long (maybe not even until the end of the literal day). It's really Fridge Horror more than a Headscratcher, though. Viola seems to recognize that Ellen isn't going to be able to pull it off in the long run, which is part of the reason for her concern for her father. While Ellen is very old chronologically, she seems to be stuck mentally and emotionally as a very disturbed child. It's unlikely that she thought through the likely outcome of her actions. Even she apparently knows that she's eventually going to go back to her old lifestyle, since in the Pseudo-Third Ending she states that it's not so bad being powerless for awhile. She's probably just going to end up doing that long before she intended when Viola's father realizes that what he brought back is an abomination.