For the first: The upkeep of a system like the one in Animus would require a ton of time and energy, so it would overall be easier to just return her to a... well, not flesh-and-blood body considering the canon, but her form prior to her last game. In other words, yes, that's fine! If you'd like to tack it on to her debt, that's more than fine.

The second we'll leave up to you. You could freeze her Soul Gem entirely or just slow the progression of the corruption, both in exchange for a heftier debt. We definitely wouldn't say no to a Witch player plot farther down the line if that was something you wanted to do!