Thompson was sent to Victoria Park by Dennis Wise last month with the instruction to improve his fitness and has made three appearances for Hartlepool, scoring from a trademark free-kick in their 4-0 win over Luton Town last weekend.
The 34-year-old has been troubled by calf and hamstring injuries this season, and his limited involvement left doubt over whether his one-year deal with Leeds would be extended before it expires in the summer.
But McAllister plans to use Thompson's quality from set-pieces and harness the additional creativity that the former England international provides in midfield.
Thompson will return after Hartlepool's game at home to Cheltenham Town a week tomorrow.
McAllister said: "The thing that comes to mind when you mention Alan is set-pieces.
"It was well documented in Howard (Wilkinson's) time here that we spent a lot of time on set-pieces, and we got our just rewards.
"It's a philosophy that I've carried on. If you repeat and repeat and repeat, and work on the quality of set-pieces, you get rewards. Alan's got that delivery."