The problem with crating cats is that you make them feel trapped. Cats usually HATE to feel trapped. That's why mine run a mile away from the cat carrier when it's brought out. Also why they meow at any closed door. If I want my cat to leave me alone in the bathroom I just threaten to close the door on them. Usually that gets a kitty to run from the window sill and seek refuge in the big house.
When I had an issue of possible misdirected aggression, I did sort of force my kitties to be together. But that was by allowing both to have free access to the house. I only contained them in a room when they were outright fighting/wrestling with each other. That was to keep them from coming to blows and hurting each other. When they were just stalking, growling, and hissing, I either ignored them or created a distraction so they'd disengage.
Some folks were advising me to separate them for a long period (a few weeks) then do reintroductions. Others advised I not keep them apart too long or I'll accentuate the distance in their relationship. I used my own best judgment by observing the situation.
As soon as I was able to get them over their initial emotional reaction and past the outright war stage, I felt it was best they be forced to live together. They each had safe areas to go run to and avoid the other cat if they wanted. But food was still served in the same place and the litter boxes were on the same floor. They got positive reinforcement and equal attention to encourage the good behavior and sharp reprimands or time outs to negatively counter the bad behavior.
Within a week they went from fur flying enemies to cuddle-bunnies again. I think it depends on your particular cats and the kind of relationship they had before. Mine are naturally cuddle-bunnies with each other.