Who gets the apartment?

There is no easy answer: it *always* depends on the full circumstances and how the judge you get (assuming you don't voluntarily work it out between yourselves) sees things. There are factors both for and against her retaining the unit:
FOR: if she has MS, moving may be very difficult and stressful for her (and stress makes MS worse); that argues for letting her stay.
AGAINST: it may be more space than she needs and, based on what you write, more rent than she can afford; that tends to argue in favor of her moving (though the court could also order you to pay part of her rent as part of any support you have to pay her, and/or simply give her enough spousal support to cover the rent). That you lived there long before marriage also argues in favor of you keeping it.
Other factors to be considered: where do you work--is the apartment particularly convenient for it (good for you)? Where are her doctors--are they close to the apartment (good for her)? Does she need or get family support: if so, where does her family live--near the apartment (good for her) or far (good for you)? You don't mention children, but if there are any, then whomever gets primary custody will likely get the apartment, so as to not relocate them.
In short, you can't predict in advance exactly what will happen, unfortunately.