At the end of the 2007–08 season, MacGregor required a hernia operation after the away game in April against St Johnstone. He was out after this operation he was out for approximately six months before making his return to the first team against Clyde in Morton's first win of the season on 18 October 2008. When MacGregor came back into the side in October 2008, he was played in the right back berth, which earlier in the season was filled by Alex Walker.