We just went through this and the short answer is no. You have to reboot the server. We had MS come on-site to help us and they were only able to get the counters back on half of our cluster..... This is a known issue app. and has to do mainly (I think) with the fact that perfmon was running when the services were stopped/restarted.
I would contact MS and see if this is covered in your agreement with them....