The logic here is simple, these are bosses key to game lore and killing them not only takes an enormous amount of effort (or in the case of Kil'Jaeden, banishing him back to where ever he came from) but it also has an effect on the world itself. Think of the impacts the events of the Sunwell had - phasing was never implemented there, and definitely should have been once Wrath was released.
Now I know you will be thinking: "Why should we only kill a boss once?" I'm not suggesting that once you kill the Lich King, for example, you are locked out of killing him again. Rather that his death triggers a change in Azeroth - which is where the phasing comes in. Icecrown Citadel could collapse or be recycled by other NPCs, such as the Ebon Blade. Once this happens, you could then walk in, click on an NPC and 'relive' the fight in the form of a new raid. The same thing could be done with the Sunwell, for example, and it could open up a new quest chain and further the game's lore in new and fantastic ways.
We've already seen how phasing can change Northrend, just look at how it's used post-Wrathgate. How do you think it could be used (particularly considering that the new expansion is called Cataclysm) to change how we play, the bosses we kill, and how we raid?