This is a really awesome problem! I tackled this for my work at TempoDB and ended up going with the Q-Digest algorithm although I took a good look at CKMS. Really cool to see this implements merging streams, I remember reading that CKMS was more difficult to merge streams than Q-Digest.
If anyone is interested this was my write up for algorithm selection: http://blog.tempo-db.com/post/42318820124/estimating-percent...