They definitely weren’t certain, and I think that’s what makes the decision so crazy. Tony and Bruce weren't really creating Vision from scratch. JARVIS was already a known quantity. He had spent years protecting Tony, working with the Avengers, and choosing to help people even when nobody was forcing him to. The unknown part was what would happen when that consciousness was combined with the Mind Stone and a completely new body. And Bruce understood the risk. He was basically the voice saying, “We have no idea what this thing is going to become,” especially after what Ultron had just done. Tony still went through with it because the alternative was leaving the body in Ultron's hands. He was taking a huge gamble, but he wasn't gambling on a random AI suddenly becoming good. He was trusting that the core of JARVIS would survive the transformation. And he got insanely lucky that the being who woke up was even better than JARVIS.

I still don't understand how Civil War split the Avengers over the Accords, then in Infinity War Cap walks into the compound a wanted fugitive and Rhodey ignores Ross's order to arrest him. Vision's beam crippled Rhodey. Why wasn't he angrier?