I use ebay/Fabio in a similar pattern as Linkerd and it's been amazing. I can understand that it's very useful to also have the latency stats and circuit breaker features like netflix/Hystrix.
There are also more and more private networking / tunnel / sdn tools popping up, I wonder which of the techniques will win out. There are advantages to not doing too much in each tool.
It's useful to separate traffic to instances/services by need-to-know e.g. admins vs users, and that would require two instances of Linkerd to truly separate the traffic. In this case I use VLANs/SDNs with service discovery instead.
Always interested to hear how others are solving this routing problem.