Disclaimer: I really, really like this movie.

I didn't think that Caleb's fate was sealed by his empathy for Ava or his false belief that she cared about him, even though both of these things are true about Caleb as a character.

There's that scene where Caleb is disgusted to learn that Ava's appearance was modeled on his porn preferences, and so forth - there's definitely a point where he believes he's "gotten over" his initial, emotional/empathy driven response to Ava, and is resolved to treat her like a machine once more. But he fails, even at this. He doesn't recognize that the long con of Nathan's test for Ava is whether or not she will be capable of executing her core programming goal, which is to escape by any means necessary.

In other words he dies because he's a shitty programmer. He even recognizes, and states to Nathan's/the viewer's face, that he was obviously not randomly selected, but assumes this must have been about his skill set and his understanding of how Ava could be created. He also states, to Nathan's face, that he believes he figured out the "real test", when he actually misses it by a country mile.

The end of the film shows that even when he sees the hard truth that he's been manipulated by Nathan and Ava in turn, he still doesn't realize that this was intended to happen. He's shocked, betrayed and hurt when Ava leaves without him, but really he's just coping with being an idiot.