McCartney is out for the rest of the season after he hobbled off with the same knee injury that had kept him out of the previous four months.
"I would have thought (he will miss the rest of the season)," Allardyce said of the left-back.
"It's a recurrence of the same injury, his medial ligaments, which is a very big disappointment for him and for us.
"That was the only downside for us today. Otherwise, it was a great day for us.
"It was a great performance and it takes us ever closer to that safety margin."