Is it permissible for me to cover the 'awrah of a worshiper if he has raised his trousers to mid-calf?

If the trousers were originally above the ankles and the worshipper then folded them up for prayer, this is considered kaff al-thawb (tucking up garments), which is prohibited. The person may unfold the fold unless it causes fitnah (temptation/strife).

However, if the trousers were originally below the ankles and the worshipper then folded them up to raise them, the fold should not be undone, nor should the person be criticized, because raising garments above the ankles is legislated.