Valdes, who will be a free agent at the end of the season, announced on Thursday that he would not be signing a contract extension at the Camp Nou.
"We have to respect him, he is our goalkeeper and while he is with us we will have to help him and it would be nice if he could have a good exit from the club," Vilanova told reporters. "He deserves it for everything that he has given to the club.
"During the last few months I have seen him be very happy, I don't think that he is upset with us. This is not about money, talks didn't even start."
Valdes signed his first professional contract with Barcelona in 2000.