The keeper was surprisingly dropped for the 1-1 draw at Priestfield as Jackett opted to go with Alex Bass between the sticks.
MacGillivray has been linked with the Scottish giants and supporters were left asking if that was the reason for him dropping to the bench.
But Jackett stated it was a decision based purely on footballing matters.
He said: ‘It wasn’t (the transfer talk a factor in his decision).
‘We haven’t had any bids or enquiries and it’s not one we’re necessarily inviting either.
‘It purely was the right player for this particular game and was in no way linked to anything behind it.’