Hi, Tony
Yeah, that's the tool. And there are two methods to clear up pink dots. Using that special tool and using chroma smoothing thingy. The PDR tool is best but you have to know the exact resolution of the frame since the dots are manually programmed according to the position of the PDAF on the sensor.
The chroma smoothing sometimes leave artifacts on magenta colored stuff.
the Raw Therappee cleanup is basically the same as running a magenta defringing on lightroom/ACR, but you'd need a strong defringing, causing artifacts on the fringe of everything magenta. Plus sometimes it leaves black dots when you sharpen the pic a bit
This is applicable with cameras that has EOS-M hybrid AF sensor like the 650D and 700D. (and the eos-m itself) since MLVs recorded from them also records the AF points.
Would be nice to have this function batch executed when waiting for the DNGs to complete.
Btw, did you get the jar from the github? (I think the one linked in the post is outdated)
Also, for clarity: Alex's PDR is the raw2dng cs2x2 and it works great too (I think this is the latest one:
http://acoutts.com/a1ex/raw2dng_cs2x2_ahdlike_noise.exe)
PS: MLV has --cs2x2 too (no idea how good it is though. Never tried it.)
Any of which gets implemented would be great though.

(I guess MLV's --cs2x2 would be easiest?)