Apologies in advance if I'm mistaken in my lore here, I am not a Sith expert.
I think politics played a big part in why Malgus wasn't on the Dark Council (please correct me if I'm wrong and he actually was at one point). In the lore I've read, he went against the Council on more than one occasion. He was successful in what he did so it was overlooked in terms of punishment but it was something that wouldn't sit well with a lot of powerful Sith. He also was married to an alien, even if he did eventually kill her, and the Sith are racist enough to hold that against him.
So you have a very powerful and very skilled radical who had ignored your authority before and has widespread support among certain parts of the military. I think they took a look at that and assumed that the second he was on the Dark Council, it would be bloody coup d'etat time.
It might have been a smart move to put him on it though. Making him part of the system might have blunted his radical edge a bit and made him try to work within it, but I don't think the other Sith on the Council would be willing to take that risk.
Your knowledge is perfectly sound here. I agree, Malgus was a radical and while I'm not actually sure, I expect he went against the grain more than once. What I know for certain though is that he was disgusted by the political backstabbing and manipulation occurring in Sith politics, and was fairly disinterested in it - more of a front line warrior.
Despite this, I'm still surprised he wasn't placed on the Council. I don't think he would have passed up a seat on the Dark Council if he was offered it, if he really was committed to cleansing the Empire he would have seized such an opportunity to reform the Empire from within. What's more his views and Darth Marr's were almost identical, he'd definitely have ally there. And seeing as Marr is the de facto leader of the Council, I don't see why Marr didn't have him appointed...