It's been a while since I finished the Dark Brotherhood questline but I don't believe you ever learn exactly why you had to kill Rufio. Just know he's your only ticket into the Dark Brotherhood. Also know he sleeps 20 hours a day so he's fairly useless otherwise. ;]
Oh, and should you kill him, you'll see him again, atleast in some form.
As for cheezit: I don't think there's anyway of preventing the assassinations. The storyline is pretty tightly woven around the idea of betrayal which makes it one of the better storylines in the game (atleast in my opinion). I never bothered looking around the rooms to learn about who I was killing so I didn't make that connection until much later in the questline.
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