I definitely think this feels like a Chrono story. As far as the religious overtones, I never got the idea from Cross that they were "destroying destiny." Destroying a manipulator, perhaps, but not destiny. (By the way, I am a Christian as well.) And from Trigger, I never got the feeling that Lavos had controlled the evolution of the humans. Humans had already (depending on your personal belief) been created/evolved/whatever. They were already there, though the Reptites disdainfully referred to them as "apes" in a derogatory fashion. Their minds grew through collective experience (just as we now understand things that even just 100 years ago were mysteries), and their brains "evolved" in intelligence that way. So I never bought Lucca's idea that they had evolved because of Lavos. I just dismissed it as, "She's still a human who can be wrong at times, and she's probably an evolutionist to boot."
Dismissing those in my mind, I then ended up feeling that the Entity was really more God than the essence of the planet. (I'm not about to get into a religous debate, so don't start with me there.) In other words, in the end, I felt that it promoted humans' dependence on God in that (since it seems the Gates were made by the Entity and not Lavos) without Him, there can't be any way to win out and survive.
So all in all, I didn't really have any objections to the idea of "destroying destiny by changing time" or whatever because that's not really what came across in my perception.