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...