But in many ways TES is largely focused on allowing individuals to play their characters as they see fit. This means, ideally, everything from pacifist holy person, to guardian of the weak, to murderous aspiring tyrant and most points inbetween. That people might want to take down the DarkBrotherhood but not officially join the Legion is highly probable. To be honest, I had an urge to handicap both the Brotherhood, which I found vile, AND the Legion, whose members I found unsufferably sanctimoious in many instances. Personally, for quests that are potentially for the greater good of the region, I think it would be good to have freelance options AND faction options for dealing with menaces like The Worm Acolytes and The Dark Brotherhood. I.E. You can join the mages guild/legion and have it as part of their main quest, along with other advancement options, or you can follow a different quest path with the same ultimate initial goal of hamstringing these nefarious agencies, but as an aide to rather than member of their opposite numbers.
As to Rufio. . . he may have been a murderer, but there is no code or precondition with the Dark Brotherhood that requires all their marks to be members. With the right offering of gold and invocation, you could hire them to kill some former friend who didn't pay you back your loan of 50 septims, or some lecher employer who groped your buttocks one time too many, or some neighbour who keeps putting the refuse from their yard into yours or who you've caught pilfering cabbages and lettuce from your garden. The amorality of the organazation is so severe and chaotic that it really does trend towards the worst kind of immorality. That they occassionally and inevitably kill some people who really did have it coming does not wash away the veritable river of essentially innocent blood that they have spilled and will keep spilling if left unchecked.
Ah.... that last paragraph in particular was beautifully written - well done.
I agree with pretty much everything you said there, with only one proviso from what Velorien has written - the morality in the game should be that of the player and/or the factions the player joins - not one imposed by the game overall (and I don't think or mean to imply that you disagree with that point - I'm just following a path your post set me on). I'm not much impressed by moral relativism as a general rule, but certainly within the limited confines of a game, and particularly with the understanding that, as you note, people are going to want to play any of a range of characters, morality should be treated relatively. If your character joins a faction that considers another faction evil and shares that view with them, or even if s/he just holds that view and decides to freelance, that should be possible in the game. The more things of that nature, the better, as far as I'm concerned. And to nod toward the distinction that Velorien made, if there are others who consider your character's actions to be the evil ones - great. That just adds more spice. Granted that that sort of complexity would be difficult to pull off in a game, I think it's definitely something toward which to aspire.
And as a bit of a side note on moral relativism, I've always been sort of amused by the people who jump into the DB line in Oblivion, get to the Purification, then are suddenly repulsed and saddened by it. To me, that's the real test of an assassin, and those who have a problem with it haven't actually come to terms with the amorality of the organization. And I have no doubt that that particular turn of events was included in the game specifically to make that point.