I think he, demoralized by the "incident", will feel that others should control the Avengers and decide. Both Vision and Scarlet Witch are afraid of losing their humanity, I strongly believe that, as in the comics, Chthon is the source of Wanda's power. Remember she is not sure who she is, either. I do think Vision will be conflicted in the movie and will be shown to be not some infallible Jesus figure, but in fact a sentient being who errs and misjudges like any human. He is, by his own admission, naive, and does not know what he is, putting him at a disadvantage when others, such as Stark, are making and pushing their agendas. Another fascinating thing, Stark is a kind of "father" to Vision, just as Cap is a "brother" to Wanda. It is through his relationship with Wanda that we will see him come to accept himself as a person, and its probably the thing that makes the other Avengers truly accept him as such too. Note that it is Wanda and Thor who most view him like a normal person, and will most likely be at his side when he faces Thanos.