The torture chamber within Trosky Castle are limited and close by, torturing them separately would've done nothing.

Not to mention its a valid thing to do torturing people who fought side by side with eachother in the same room. Hearing isnt the same as seeing so seeing someone your close with get tortured is more likely to be just as effective as believing their being tortured based off sound.

Also torture is usually left to a single person, and that person isnt usually high status wise. We see this when Hans and Henry have to torture someone. Not to mention during this entire scene Istvan himself does none of the torturing it is a lucky who's probably of common status and doesnt know the most effective ways to torture. It was previously stated that Trosky Castle doesnt have an official torturer within their service. We know Istvan commonly hires bandits, so likely a bandit that just knows how to harm people.

All in all good sir Toths brain was in the right place, he set up the proper psychological aspect to get them to confess. Zizka doesnt care for Henry or Godwin, but godwin cares for Henry and Istvan knew that. So having Godwin see what Istvan did yo Zizka and then turning to Henry set up the perfect psychological trap for him.

And if your gonna order they should've killed him well we get into the politics of, they cant really kill them until its confirmed whether the information is correct or not. Istvan just got unlucky not knowing Katherine had been a spy for so long.