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...
All right! Not completely wrong!
That is interesting, what you said about Darth Marr. It might have been that Marr didn't know Malgus' intentions as a reformer; I'd imagine he hid them well. It might also have been that both Darth Marr and Darth Malgus wanted to the "the one" to change the Sith Empire, not "one of the ones," if that makes sense. There's a pretty strong only one person at the top thing with the Sith, even if they're run by a council while the Emperor's on the can (or whatever he's doing).
Not to break from lore, but I suspect is the main reason is that the writers and developers didn't want Darth Malgus on the Council for the whole False Emperor thing or other storylines. So even if it made sense, they wanted to keep him as an inside-outsider.