It looks like there is a lot of good advice on this thread for how to mitigate the configuration problem (bamboo, consul template, etc ...) but then you run into reloads, and even if you use zero downtime restarts as I described in my HAProxy deep dive (http://engineeringblog.yelp.com/2015/04/true-zero-downtime-h...), you still end up with periodic ~50ms blips in your timings.
We've found that Synapse (https://github.com/airbnb/synapse) is best in class at managing HAProxy for us in a fairly large SOA. It is really intelligent about doing as much as possible dynamically over the HAProxy stats socket as opposed to reloading for every configuration change, and we can finely tune how often we are reloading HAProxy. The best part is that it is fully pluggable. Use DNS, marathon, zookeeper, etcd, etc...: Synapse can manifest that service registration information into HAProxy configurations.