QuoteLong story short -- use MLVFS.
(or MLP or MLVProducer or cr2hdr.app -- all of these apps can deal with the focus pixels.)
QuoteSome brainfood regarding those pixels for you:
http://www.magiclantern.fm/forum/index.php?topic=16054.0
Thanks dfort and Nickfreak. After I've been trying quite a lot, I found the best solution last night.
The MlRawViewer v.1.3.3 removes the dots and does a brilliant converting into Apple ProRes.
Here's a short test:
https://www.youtube.com/embed/9g4qH-Cndco