I think Captain Atom would win here... I think Atom's matter transmutation powers will give Vision all kinds of hell here... the only thing that scares me about Vision is his intangibility skills. But will that stop Atom from altering Vision on a molecular level ? I dont know about that...
Captain Atom is far stronger and more durable than the Vision. He also has much faster flight capabilities. The Visions solar gem laser would do nothing to Capt Atom and the Capt is capable of absorbing the effects anyway.
If the Vision were to try his intangibility attack on Capt Atom, one of two things would likely happen. Either his intangible hand would not penetrate the Capt as has happebned before with beings who were composed of energy (including organic bodies filled with energy) or if he did insert his hand, it might get damaged by the enegies within the Capt's body (as has also happened before).
When the vision has flown in the past, he still has some small amount of mass (not fully intangible) as he has used the wind to push him along. If this has not changed, the Capt can use his matter control powers to damage/kill the Vision.