The amount of moire/aliasing artifacts comes from the lineskipping sensor, and there's a lot difference between different raw editors (debayering methods)
For best detailed results, you should checkout raw editor RawTherapee, it's free/open source.
It's a raw photo editor and has multiple options for debayering, in my opinion the LMMSE debayering works best for lineskipping raw video files from magic lantern.
Check out the RawTherapee workflow
http://www.youtube.com/watch?v=MweH3RAssXswww.RawTherapee.comFor a quicker workflow for getting rid of all those colored speckles, you could separate the video file in Luma and chroma channel and do a blur effect on the chroma channel. This can be done in many video editors, also in the free version of Blackmagic DaVinci Resolve software.
In Resolve, change colormode to LAB and disable the L(uma) channel, now do a blur effect.
Also, the colored speckles turn up more with wide angle lenses, and supersharp lens settings like from 2 stops closed down diafragma (f8 and f11).
So indeed, shooting with diafragma wide open can help a little, just as closing down to f16 or f22, the lens is less sharp at minimum and maximum diafragma.
That said, I shoot a lot of video with the Canon 6D and the sharp 35mm f2.0 IS and use it a lot at f8 and f11, and all color aliasing can be removed with RawTherapee.