The Rolling Stone article about Sgt. Bowe Bergdahl published in June of 2012 reported:
In the early-morning hours of June 30th, according to soldiers in the unit, Bowe approached his team leader not long after he got off guard duty and asked his superior a simple question: If I were to leave the base, would it cause problems if I took my sensitive equipment?
Yes, his team leader responded – if you took your rifle and night-vision goggles, that would cause problems.
And so Bergdahl left his rifle and night-vision goggles behind.
If Bergdahl planned to desert or join the Taliban, why would he care about getting in trouble for taking some of his equipment with him? If caught, he'd already be in trouble for much larger issues.
But if he planned to leave the base for a couple of hours and return, as it's reported that he had done previously without getting into trouble, then it makes sense that he wouldn't want to end up in trouble for taking the gear with him.
I think this evidence strongly refutes the idea that he intended to desert.