As Allison detailed, a lot of things had happened in Kael'thas's life just prior to Warcraft III, and during it. The captain of the football team steals his girl, kills his pops, and massacres the people of Quel'Thalas. Dalaran gets destroyed, and the remnants of his people are slowly falling into sickness for unknown reasons. Despite this, Kael'thas forges ahead and steps up to lead his people and protect them, no matter what it takes. This may mean allying himself with the remnants of Lordaeron, the people who indirectly caused the fall of Quel'thalas. This may mean allying with the Lady Vashj and the naga, described by Allison as "vicious," despite being what they are. For the good of Quel'Thalas and the Sindorei, anything goes.
Not only are the Blood Elves in a tight spot, Kael himself is the last of the Sunstrider Dynasty, and at quite possibly the worst point in High Elven society. It's up to him to fix things, or the entire Sunstrider Line goes to pot. It's on his shoulders not to screw it up. He's shown the capacity to do whatever it takes to preserve the Sindorei through his alliances with Garithos and Lady Vashj, and later Illidan. None of these individuals were good people. None of them are benevolent, and certainly they don't have the Blood Elves' best interests in mind. They were, however, useful to Kael'thas at the time the alliances were formed. Power, protection, a means to survival. Kael'thas did not ally himself with Illidan because they were of one mind, or because he even believed in Illidan's cause.
-The Frozen Throne
Kael'thas' loyalty to Illidan was based only in that it would benefit the Blood Elves. Illidan, to Kael'thas, was the source of a cure for his people, nothing more.
The above dialogue comes from the Magisters' Terrace, the 5-man dungeon on Quel'Danas. His statements are perfectly in line with his actions since he first appeared on screen in Warcraft III. Again, I'll state that I think they could have done this storyline better than they did in the World of Warcraft, but I don't think there's no evidence that points to this outcome. The piece of the puzzle that is missing from the picture is the point in which he completely fell to the Legion. It's my belief that Kael'thas was out to manipulate the Legion and use them for the Sindorei's survival, but was ultimately unable to withstand the pull of the demonic. The Burning Legion was to be just another tool to revive his fallen people and cure them of their ailments, but Kil'jaeden is not as easily used as those Kael'thas stepped on in the past.
I fully believe the direction Kael'thas has taken in the Burning Crusade makes sense for his character, but I won't disagree Blizzard did a poor job putting that out for all to watch. Hopefully, this is another example of the WoW team being protective of their heroes, and we won't run into it again in Wrath of the Lich King.
All along, since we met Kael'thas, he has done what he's done because he truly believed it was in the best interests of Quel'Thalas and the Sindorei. That belief ultimately led him to the Legion, the point of no return. Tragic, really. He's been under the impression since day one that he was doing good for his people, but in the end, it became his undoing.
This is just my interpretation, of course. I think it's pretty close to the intended story there, but most people are pretty content with "lorelol" which is a distinct possibility! I happen to prefer this view of it, personally.