If Ryou's health was paramount in the end of the Yuugi v Bakura duel in the Battle City finals, Yuugi shouldn't have attacked, regardless of whether it was Ryou or Yami Bakura running their body. Ryou was going to, and in fact did, take the hit regardless.
If making sure Marik's grand plan didn't work (slash saving the world, though I'm not convinced the world is at much as risk from that plan as Yuugi et al seem to think) was paramount in that duel, Yuugi should have attacked without more than a moment's hesitation, again without caring who was in control of Bakura's body. Yuugi needed to win that duel, and endangering Ryou would be a 'needs of the one don't outweigh needs of the many' choice—that for bonus points Yami Yuugi as Pharaoh should have been used to making, even if he doesn't recall any such instances. Sucky choice, of course, especially for Ryou, but.
Neither scenario, of course, is how the duel ended. So what was going on in that episode?