Gills striker Cody McDonald bagged his 24th goal of the season with a minute to go after Phil Jevons' controversial first-half penalty had seemed enough to give the Shrimps all three points.
McIlroy said: "Coming here you'd be absolutely delighted with a point but my players are absolutely gutted.
"We had a gameplan and it was three minutes away from working. They scored a good equaliser I think - it would have taken a special equaliser to beat Barry Roche. My lads gave me 110% and their work ethic was fantastic.
"Even though we got the one point when three was looking on I'm delighted with it, and hopefully that now will be enough for us.
"We had our stall set out - we knew exactly what to do and my lads did it to a tee."
Source: PA
Source: PA