Defender Maguire was initially named by England manager Gareth Southgate in the squad for next month's Nations League games against Denmark and Iceland, but was later withdrawn following the guilty verdict on the Greek island.
Maguire received a suspended prison sentence of 21 months and 10 days, but maintains his innocence and has been granted a full retrial after appealing against the verdict.
"I thought there was no way Gareth Southgate could name Harry in the squad he announced on Tuesday, but he did," Rooney told the Sunday Times.
"It would have been more sensible to say: 'Harry has just played a very long season and needs more rest and let's wait to see what happens with his court case.'
"By jumping too quickly and putting him in the squad, it was almost inevitable he'd have to get pulled out.
"Now it looks a mess. They've picked him, pulled him out, and now do they put him back in the squad? Because as things stand he is a free man and innocent!"
Maguire was found guilty of repeated bodily harm, attempted bribery, violence against public employees and insulting behaviour.
In a BBC television interview on Thursday, the 27-year-old maintained his innocence, describing how his younger sister Daisy had been attacked in a bar on the island by two men who drugged her, and that he had feared for his life.
Rooney said he was convinced the truth would come out in a retrial and that Maguire would clear his name.
"Often in our country we rush to conclusions and judgements, and in the case of Harry we need to be more open-minded and allow matters to develop," he added.
"I don't believe that anybody puts themselves on the BBC and faces the sort of questioning he did unless convinced of their position.
"I actually feel for Gareth a bit because he was trying to show loyalty to Harry -- but I'm sure if he faced the same decision again, he would make a different one."