The former England international has been troubled by injury throughout this season but his fitness held impressively at Hartlepool, where he featured seven times in the space of a month.
Thompson's encouraging form at Victoria Park led McAllister to confirm that the 34-year-old - sent out of Leeds by former boss Dennis Wise in January - would be included in his plans at Elland Road.
But the ex-Celtic captain completed just 12 minutes of United's 1-0 win at Swindon Town on March 1 and has not been available since.
McAllister said: "The injury has moved into his calf now as well. It's frustrating for Alan because he went away and played nearly every minute of every game at Hartlepool and trained every day.
"He's come back and it's been one little niggle after another. But I've had a good chat with him and as we get into the final push, I feel and he feels that he's still got a part to play before his contract ends at the end of the season."