Rooney, 31, ended his 13-year spell with United to return to his boyhood club earlier this month in a deal which helped smooth Romelu Lukaku's move to Manchester. England's all-time top scorer was notionally valued at £10m by both clubs but United opted to waive a prospective fee due to the intricacies of the Lukaku deal, which could potentially be worth £100m.
Rooney's influence waned during his last couple of seasons at United and had to make do with a peripheral role under Mourinho; he only started 15 matches in the Premier League last season and was consigned to the bench for much of the campaign.
But Mourinho had hoped to keep the Croxteth-born attacker, who is primed to make his second debut for Everton on Thursday (27 July) when Ronald Koeman's side face Slovakian outfit Ruzomberok in their Europa League qualifier at Goodison Park.
"I miss him a lot," Mourinho told Sky Sports. "I think he's a fantastic guy. I'm not the kind of guy that gets normally emotional in my job and I did it with him when he left. But I'm sure that he's going to be very, very good for Everton and Everton is going to be very, very good for him.
"It was not difficult [to let him go] because he deserves that, it's not difficult. He deserves what he got and what he got was our desire for him to stay and our respect by letting it be completely clear that we would like him to stay.
"And at the same time, the respect that allows him to be happy - allow him to try to play every game, every minute which honestly I think he needs. At his age, I think with his genetic, with his body, with his personality too, I don't think he's the kind of player to be less motivated, not so happy because he's not playing every minute.
"I think with his body he needs to be working at high intensity every day, every match. So I think he deserves that respect from us: if you want to go, we have to make it easy for you to go."
United may have made it easy for Rooney to return to Everton, but they are finding it difficult to bring new signings to Old Trafford. Lukaku and Victor Lindelof have swapped Everton and Benfica for United respectively this summer, but Mourinho is still after two new signings in order to provide "balance'"
The two-time Champions League winner is pursuing another central midfielder, with a move for Chelsea's Nemanja Matic in the offing, while a winger is also on Mourinho's agenda with links to Inter Milan star Ivan Perisic refusing to go away.