McCartney came off the bench in the 78th minute to make his first appearance since suffering medial ligament damage in his knee four months ago but hobbled off 15 minutes later after suffering the same injury.
"I would have thought (he will miss the rest of the season)," Allardyce said in his post-match press conference. "It's a recurrence of the same injury, his medial ligaments, which is a very big disappointment for him and for us."
He went on: "We are disappointed for him because he has waited so long to get back, and get on the pitch.
"We thought we would give him a run out and give the lads who had done so well a rest, but sadly he went down with the same injury."
Andy Carroll scored twice and Gary O'Neil also got on the scoresheet as West Ham romped to a morale-boosting victory over the Baggies, who grabbed a consolation penalty through Graham Dorrans late on.