If you ask me, there was little point in getting Beast's nobody... wasn't their goal to NOT be Nobodies anymore? And, had they "asked" Sora to defeat the Heartless for them, there wouldn't have been much of a point to attack Hollow Bastion. Of course, more or less I'm just joking around - we all know the game would have been much worse if what I'm suggesting actually happened.
The fact that we were meant to believe they were evil from Yen Sid alone and without reason is what is actually bugging me here. Think about it - Yen Sid never being in the game, and the first we see of the Organization is Xaldin at Beast's Castle. From that single encounter I would have immediately realized they were "evil" people doing "evil" things. I think that because Yen Sid told us they were evil, and we saw very little of it for the first half of the game (and I still felt little afterward), we all find it harder to link that they were evil, especially when discovering their goal.
I know during my first encounters with Demyx, Saix, etc. I kept trying to piece together what they were doing evil - Saix told Sora to BE CAREFUL! How is that, alone, evil? Yes, it went towards their goal, and yes, some things to get to that goal were questionable, but to the person playing through the game for the first time it is REALLY hard to picture guys like that as being evil.
So are they or not? I've decided it really is just too difficult to tell, because there really WERE a lot of instances where I felt they weren't doing anything wrong and Sora wrongly went after them (*cough*becauseyensidtoldhimto*cough). There are exceptions - Xaldin at Beast's Castle, Luxord in Port Royal (even that I find hard to see as "evil," what he did was just annoying). Then Xemnas wanting to apparently take over the universe. As for other members, like Saix, Demyx, and Xigbar even, I REALLY didn't see why, during the main course of the game, Sora went after them.
So, I guess you can look at it like this: Their goal wasn't evil, but about half of them seemed to do evil things to reach that goal, while the other half didn't seemed to do evil things other than fight you, and imo Sora seemed like the one egging the fight on. In total, I'd say NO, as a whole, the organization was not evil. Were they intended to be? I'm sure they were - but that has more to do with the writer...