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Long story short -- use MLVFS.

(or MLP or MLVProducer or cr2hdr.app -- all of these apps can deal with the focus pixels.)

Some 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

I love the ML for the 100d!

But I'm not sure if it's just me or my camera, but I get these coloured dots when recording RAW-video (see picture below).
First I hoped it would be fixed in a later update, but it's been the same through all the nightly builds since first release.

Any ideas on how to fix it?