The Australian was dismissed in the 90th minute of their 2-1 defeat at St Mirren, after referee Brian Colvin had deemed him to have elbowed Saints’ youngster Thomas Reilly.
The result means Well face a scrap to avoid the drop from the Scottish Premiership, and they will now take on one of Hibernian, Rangers or Queen of the South in a two-legged play-off encounter.
But boss Baraclough is hoping to have the 31-year-old in his side and will appeal Colvin’s decision, saying: “For me it would be a travesty if Scott misses the next three games because I thought it was a poor, poor decision.
“I’ve watched it back. He’s not made contact, he’s not gone maliciously to make contact and when the officials see that they will probably agree as well.
“We will definitely appeal. It wouldn’t be a frivolous appeal either. It’s a massive call at a crucial time of the season.”
As for the play-offs, Baraclough added: “I’m confident we can deal with whoever we get.
“I’ve seen all three teams and I’ve got no reason to believe we will be the underdogs going in to them.”
John Sutton opened the scoring from the penalty spot on 76, before Mark O’Brien put through his own net to allow Saints to level. Stevie Mallan fired home a late winner, after McDonald was dismissed.
Meanhwile, Saints boss Gary Teale said Alan Gow had suffered a heavy knock to his head, following a collision with Well defender Stephen McManus: “He’s not too good and will have to go up to hospital.
“Hopefully it’s just as a precaution. He’s a bit spaced so needs to get checked over.