But he hopes the improving side can rise above any niggling tactics at Suncorp Stadium as they look to seal the three-Test series 2-0.
Swain will miss two games after headbutting a niggling Jonny Hill, who had tugged at his hair and triggered the Australian lock late in the first half in Perth.
Australia went on to score three second-half tries despite playing with 14 men, snapping an eight-game losing streak against Eddie Jones' side.
"We've got to focus on what we can control, what we need to do on the field," Hooper said of the expectation of more niggle.
"There's plenty of roles on the field in transition, you can't be getting sucked into that.
"But it's part of the game and the smarts around how you come out on top of that is important.
"It's always a factor and dealing with it in the right way is going to be a challenge, but a good one."
England will also debut former Sydney Uni captain Guy Porter in the centres, while winger Tommy Freeman will also earn his first cap as Jones looks for more "punch" from his backline.
Hooper said they'd be too occupied to sledge the Australian-raised Porter, who was born in England but moved to Australia as a seven-year-old.
The set piece battle looms as crucial with the return of Taniela Tupou for Australia, while Jordan Petaia has a chance to take ownership of the No.15 jersey after injuries to Tom Banks and Andrew Kellaway.
England assistant Richard Cockerill stoked the battle of the front-row and promised his men wouldn't shy away after a series-opening loss.
"We know when we have to turn up when the moment comes, and there will be lots of those moments," he said.
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