I was really trying to play a "good" character, but long story short, Belethor pissed me off for the last time. I often visited his shop to sell little odds and ends that wouldn't sell at the other, more specialized shops. Now that he's...not with us any more, will someone step up to take his place? Or will I need to find a new shop to frequent?
Once you kill a non-important character in the game, that character will be dead forever.
As for the shop; if one exists, it is possible that a relative takes over the shop and quests.
Source: Game Informer Cover