Spoilers ahead:
Interesting comments. I think he takes it a little too far however. Quorra was clearly checking how well Sam filled out his costume on their little drive to his dad and that doesn’t really fit with an analogy of the relationship between Christ and the church. There was no hooking up between them because they wanted a PG rating.
I saw it more as an allegory of the Book of Revelation. The programs knew Flynn was their creator, but they were in rebellion against him. The result was the end of their world and the lifting of the one was faithful to them up to ‘heaven’.
Spoiler:
Adolescent children check each other out without fully understanding why their doing it. I maintain that Quorra’s admiration was innocent. Consider the ending and how her focus was on the world she had transcended to. Kissing is PG, yet there was none.