Rooney rejoined boyhood club Everton following a hugely successful 13-year stay at Old Trafford which saw him win every trophy available to him and surpass Sir Bobby Charlton as United's all-time leading goalscorer.
The 31-year-old will return to Old Trafford for the first time since his departure when Everton visit on Sunday, and Mourinho insists that allowing the former club captain to move to Goodison Park was simple due to the player's desire to leave.
"I think it is easy. When the legend decides. I think so [it is the legend's choice]. That way it is easy because you don't have to think a lot," he told Sky Sports News.
"You just have to respect the player's desire, and what they decide. And when they're a legend they deserve that freedom of choice."
Rooney scored 253 goals in 559 appearances for United, helping the club to 16 trophies including five Premier League titles and the 2008 Champions League.