Glad they are alive, but sorry to hear you sister and BIL are suffering as a result of this accident. Most important: does she have an attorney who is dealing with this for her? If not, that would be my first call in the morning, especially since she has ongoing medical issues.
Regarding MBFS: yes GAP will make them whole, and according to at least one report she may be entitled to any equity/overage (but as you mentioned, have to check the lease contract with MBFS can provide)
The MB gurus might have more insight. I hope she gets all the care she needs and has a speedy recovery (which is undoubtedly longer than a few weeks).