My neurologist has urged me to stay on tysabri (natalizumab) despite the risks of pml (positive to jc) is this a hint that my MS is much worse than I thought?

Management. The risk of PML becomes more significant the longer you take Tysabri, (natalizumab) and 2yrs is the turning point, but risk is still low, about 1 in 90. However, for some pts, this still is too high, and they switch to Gilenya at 2yrs. This is a calculated gamble, and should be your decision, not just your doctor's. The severity of your MS is just one part of this, so talk at length with your neurologist.
Many things. Many things go into a decision like that. And by the mere fact that you're treated with tysabri (natalizumab), (natalizumab) i would assume you are seeing an ms subspecialist, not a general neurologist? You should ask him/her why tysabri (natalizumab) is the best med for you at this time.