I think your take on it is reasonable LordPsycho. Certainly no-one outside the Inner Circle of the Unforgiven chapters knows about the Great Betrayal and the hunt for the Fallen. I think the general lack of co-operation between the Dark Angels and the Inquisition spreads a little further, but then they are hardly the only one of the older chapters to hold themselves aloof of Imperial politics.
Maegon certainly wouldn't have any idea about the Dark Angels true darker side (as he wouldn't be alive if he did
). However he might well be aware that the Dark Angels are rather secretive and don't exactly have a history of co-operation with the Inquisition.
The disappearance of Inquisitors who put their noses where they aren't wanted would similarly always have been done in such a way that nothing could be definitively tied back to the Dark Angels/Unforgiven. It is not implausible that there might be suspicions that they somehow had an involvement, but no-one could prove anything. Rather like how skilled politicians always seem to manage to come out clean after things hit the fan.
