First of all, Logan was angry when he found out that Xavier was controlling Jean. He didn't think that was right. He wanted her to be free, but he didn't know what that meant until after she woke up. Yes, then he wanted the old Jean back, but he believed that's who she truly was underneath, if only she could be reached and saved from Dark Phoenix ("she's not herself" he insists to Storm when he's going off to track Jean down). I think he believed it possible that she could be her good self without Xavier's mind controls.
Second, I'm not saying that it's overtly stated anywhere that Scott wants to control Jean. But in the extra footage from X1, Logan insinuates to Jean that both Scott and the professor are holding her back. He was certainly right about the professor, and from that I think we can reasonably speculate that he was also right about Scott. Are we really to assume that Scott knew nothing of Xavier's mind-controlling of Jean? (And if so, that would demonstrate that Scott doesn't even really know the woman he loves! She is an artificial creation, or at best only half of her true self.) Anyway, in that same conversation Jean counters Logan by extolling the virtues of Scott's self-control. Let's face it -- Scott's the type of guy who places a lot of value on control. I'm not even saying that's all bad; in many ways it's good, but it would predispose him to accepting that Jean, the woman he's about to marry, being mind-controlled to some extent by Xavier. He's not going to have the same kind of problem with that that a wild, untamed spirit like Wolverine would have. Wolverine would probably rather see her dead than an artificial person in a cage, because he, too, hates cages ( "sometimes when you cage the beast, the beast gets angry") and lo and behold, in the end of the story, that's the choice he makes. He would think it more humane.
The intense beauty of it all is that we do know that, even when Wolverine sees and knows Jean/Dark Phoenix for all that she is, he still loves her. Completely. And that has to be the truest of true loves -- to see the good, the bad, and the very ugly in someone, and to love them still. Logan was ready to die for her -- Jean, Dark Phoenix and all.