Are there any recommendations for flying with a severe disability?
As you say she is paralysed I assume she is unable to walk even very short distances. If this is the case, she must have someone accompany her. A family member will be sufficient in this case. The crew will obviously help get her off the aircraft in an emergency, but they are not permitted to help her eat, drink or use the lavatory. According to the rule book: If she is able to look after herself, including getting to and from the lavatory without any assistance, she can travel by herself.
Make sure you book a wheelchair! They are provided free of charge, but the airline must be notified at least 48 hours in advance to guarantee that one is available. The wheelchair will be waiting for her at checkin, and a porter will wheel her to the aircraft door where she will be transferred on to the onboard wheelchair before the crew wheels her to her seat. Once a wheelchair has been requested, it will automatically be requested for all connecting flights, ensuring her mobility from checkin to baggage reclaim.
If she is not able to sit in a normal seat, or if she needs a respirator or other life support equipment you may need to book space for a stretcher. This will usually be a minimum of three full rows, possible four depending on the aircraft layout. Obviously this will be very expensive, but doing this with a major airline will usually be much cheaper than chartering a medivac service. If this applies to your sister-in-law, you must contact the airline to book as she will have to travel as a medical case. (You would also have to pay for a doctor to accompany her)
As Steve said, contact the social security administration. I'm not sure how it works in the US, but in Europe they will pay the ticket for someone to accompany the disabled, as well as the disabled persons ticket. I'm not aware of any airlines that gives discounts to the disabled.