If there is at least 5 minutes of injury time, but the team that is losing doesn't want the extra time added, what should the referee do?
What either team wants is irrelevant. Time is determined by the referee alone, and the added time exists for a reason: to make up the playing time lost by excessive stoppages. The time should be added on, and played out.
A sensible referee may know enough about the competition to be aware of what impact a change to the score might have, but even in the case that it has no effect on any standings, should not reduce the game just on a whim.