Carroll told 710 ESPN Los Angeles that the players on those teams still consider themselves champions.
"Just watch the comments of the players. They know. They know who won and who didn't," he said. "You've heard from (Matt) Leinart and Lofa Tatupu and those kinds of guys, they all know. The whole thing is so unfortunate. It's just so far off-base, it's just too bad."
USC was stripped of its title on Monday by The Bowl Championship Series after the Trojans were hit with heavy NCAA sanctions last year, when it ruled that Bush received improper extra benefits during the 2004 and 2005 seasons and was ineligible when he played. USC's appeal was denied on May 26.
When Pat Haden took over as athletic director last year, one of his first moves was to give back the school's copy of the Heisman Trophy that Bush won in 2005. The whereabouts of Bush's own Heisman, which he said he would relinquish, were briefly in question before the San Diego Hall of Champions announced that the trophy is part of the institution's collection.
The BCS waited until USC appealed the NCAA sanctions, which included a two-year ban from postseason play and a loss of 30 scholarships over three seasons, to make a decision about its championship.
Carroll, who led USC to an 83-19 record in nine seasons but saw 14 of those wins vacated, said he was not surprised by the move, but was disappointed.
"Nothing that's happened has changed my thoughts," he said. "It's unfortunate that kids, years after, are punished for something the NCAA is dealing with from years and years before. Kids that were in junior high at the time, or in grade school, are paying the price for it."
With Ohio State now in the spotlight for similar allegations of improper player benefits, Carroll would not compare the two situations but said any decision by the NCAA would be tricky.
"I think this is a major challenge for the NCAA because of what they have done in the past here recently. I don't know how they're going to possibly make sense out of all this," he said. "It's going to be very challenging and it'll be very interesting to see what happens."
Unofficial list of free agents
What he's most interested in, he says, is the outcome of the "not-so-secret" meetings between NFL owners and players, which are expected to continue on a more frequent basis.
"This was the time they had to work through all of these issues that have come up over the years and it is a long, hard process. ... I'm optimistic we'll get to camp and we'll get going. It's already been different in the preparation and the buildup to it, but ultimately no one wants to miss football. Everybody wants to play. The owners want to play, the players want to play, the coaches want to coach and all of that.
"The effort that you're seeing in these meetings is the urgency that they're sensing that they've got to work together and they have to come to conclusions so they can make the season available for everyone."
The Seahawks, who used their first two draft picks on Alabama OT James Carpenter (No. 25) and Wisconsin G John Moffitt (No. 75) in April's draft, will do the best they can to get ready once football activities resume. Carroll -- while staying mum on the team's plans at quarterback -- acknowledged it might be harder for younger teams to catch up.
"We're building a program," he said. "We've got issues across the board as we transition our approach and trying to put this team together. There's a lot of concerns. We really need free agency to help us. We love the draft as it came out, and got to put a lot of focus on the offensive line and some young skills guys to give us some speed and competitive players."
The Associated Press contributed to this report.