Are the doctors- Lyme and MS- talking to each other? A bad relapse of MS could leave your wife unable to walk. The medication will not stop the disease. Some MS patients will progress rapidly and others slowly- with or without meds. Remember there is no cure for MS at this time.
My first action would be to confirm that the Lyme is being cured and than if your wife's problem walking is MS, Lyme, or both. For this you really need to get both doctors to talk to one another. You may have to play the patient advocate to make sure this all happens.
I will keep you and your wife in my prayers.