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What happened to those who had mutated before the Rubric of Ahriman was cast on the Thousand Sons, were they killed, did they keep their mutations, or did they turn to dust like the others (and lose their mutations). - As I can't recall if the Codex specified.

All is dust......
They turned to dust, like everyone not powerful enough
Quite simply the Rubric worked fine, it removed all the mutations to ALL of the legion. It Just worked too well, resulting in EVERYONE without some pyscic ability unable to cope with the physical cleansing, and, well, we know what happened then

Do you think it effected all thousand sons or just the ones on the planet?

 Flame-Rage wrote:
some pyscic ability unable to cope with the physical cleansing, and, well, we know what happened then

So, does that mean that those without psychic ability were not turned to dust? Or did they die with those that could not bear it?

Every Thousand Son without psychic powers was turned to dust, those with powers had them amplified massively.

Enron wrote:
Do you think it effected all thousand sons or just the ones on the planet?

With a very, almost notably few exceptions, the fifteenth legion didn't exist beyond those on the Planet of the Sorcerer's. They had close to 900 legionnaires at the time of the burning of Prospero, and those that didn't die in it were taken to the planet. The rubric occurred several centuries after the heresy and those that were members of the thousand sons were primarily located on the planet. Some had started forming war bands, but were not in any shape to take on the other traitor legions that had taken up residence around them in the eye of terror. However the fluff regarding the rubric says it affected the legion, so we can assume that it affected everyone who identified themselves as a thousand son, because we have no fluff evidence to the contrary. So it affected all of them, including ones not on planet, there just weren't that many of those.