Ronaldo, 33, received his marching orders mid-way through the first half for an alleged tug on Jeison Murrillo's hair and could now miss the emotional return to Old Trafford and the Young Boys fixture.
"Mostly because it was the 29th minute in the first half in a difficult game, to find yourselves with 10 men for a red card, that was not right.
"Without Ronaldo this has been a very important test for us," Allegri admitted.
"At 2-0, the team sacrificed itself to avoid conceding goals. We're noticing that our physical fitness is improving.
Despite scoring a brace in the recent victory over Sassuolo, there have been suggestions that the Italian champions are able to play their more natural style without Ronaldo - but the former AC Milan coach refuted such claims.
"We can't say that," he said. "Between Alex Sandro, Blaise Matuidi and himself we've created many chances.
"With Ronaldo we've been very good and we've also been very good without him."