You shouldn't refuse bisphosphonate medications if your doctor deems them necessary or stop taking them in the wake of the new warning without first discussing it with your doctor. Atypical femur fractures are very uncommon, and they also occur in people who aren't taking bisphosphonates. On the other hand, osteoporotic fractures of the spine, hip and forearm are very common and are known to be reduced in osteoporotic individuals taking bisphosphonates.
Many doctors now recommend a five-year limit on bisphosphonates, with continuation beyond five years only if the risk of fracture is very high -- for example, if you have a history of fractures, a high fall risk, and/or are very frail. The decision of how long to continue these medications requires a case-by-case approach. Bisphosphonates accumulate in bone, so if you stop taking the medication after five years, the positive effects continue to persist for a significant time thereafter.