I read the review and found it interesting. I think I can understand why many of you were so offended. But first, I think we must all remember that it is essentially a site for Christian believers, to inform them of all content believed to be offensive to them, so that they can make their own decisions about whether or not to see a particular film.
Second, I think we all need to be careful about judging others' belief systems if we don't know very much about them. For example, do we know why they believe Jean's resurrection is "unholy"? Do we know why they think that is a bad thing? I even wonder if they think certain things (open-mouth kissing, for example) are "wrong", or just something in the content of the film they think people would want to be aware of as they make their decisions about whether or not to see the film.
On the critical side, I felt this site did not do a very good job at perceiving all the good things in X3. For example, there was a laundry-list under "sexual sin" regarding the Jean-Logan lab scene, but they failed to mention the fact that Logan puts on the brakes when he sees something is wrong with Jean. I'm not saying it makes everything okay, but it is something positive that they failed to mention.
Another instance was the cited "mercy killing". It is listed as a bad thing (again, I'm not exactly sure of their angle on this), but Jean was essentially willing to sacrifice herself to prevent herself from losing control and killing masses of people. Self-sacrifice for the good of others is generally regarded as a good thing, but the critique failed to mention this.
Interestingly enough, there were several very strong Christian themes present in the story that these critics apparently missed. One is the theme of redemptive love, illustrated through the relationship between Jean and Logan. Logan's love for Jean could be compared to what the Bible says about God's pursuing love for mankind. Logan goes after Jean in order to save her from herself after she has become totally corrupted and beyond all hope of saving herself. He loves her not because of who she is anymore, but rather in spite of who she is. And so he forms a plan to rescue her, like God does with us.
Shifting the analogy a bit, Logan's killing of Jean in this story resembles God's killing of His own son on the cross -- the one must die so that others may live. But though it deeply, infintely grieved God to kill His son (like it grieved Logan to kill Jean), God did it because he wanted to rescue others from wrath.
Lastly, I want to pose a challenge to all of us. I think it is important to think about what is good and what is bad in a movie. Sure, it's only a movie, but I do believe we are able to be, sometimes strongly, influenced by such things, and it is therefore worth thinking about.