Bolded part is my point. That's why Civil War can only work INO, IMO. It was out of character for Tony to do it then, and will be out of character now.
Also, if it's true, I think this is a case of business taking over creative input. I highly doubt this would have occurred had Batman v Superman not come out. Keep in mind they originally shared a release date.
I'm sure it will be "in name only", just as the Extremis plot was only loosely based on the comics. First off, the comic Civil War involved the entire Marvel Universe, the focal characters were Iron Man, Cap and Spider-man. That's not going to happen here. The focus is going to be on Cap and Tony, with perhaps Bucky and Sam as side characters. You aren't going to see Tony do the BS stuff he did in the comics, like create a Thor clone to kill Goliath, or enlist villains to fight Cap. First off the Russo's have developed a good name for themselves, do you think they want to be known for trashing Tony?
Second of all, it's Robert Downy Jr., he's going to be acting like Robert Downey Jr., do you think anyone is going to be able to take him as a villain? At worse he would come off like Hiddleston if they really went that route and you're still going to love him. The Tony is Civil war was just a *****e, no redeeming qualities, and RDJ would never sign on to that.
As to you're last point, the word was, the plan was always to have him in, but in a limited role, but it was Downey who thought, if he was going to be in it, he wanted a more prominent role than a cameo. Now I don't believe things occur in a vacuum, so I'm sure BvS, was in the back of someone's mind.