Well, you're mixing the anime and the games in that imo. In the games, Pokemon don't go swimming or bathe. In the anime, type disadvantages don't mean much to be liberal. So a water move may hit a Fire Pokemon hard, but wouldn't immediately knock them out.
There's also the matter that a lot of Fire Pokemon don't have actual fire on their bodies, think like Vulpix. They're warm and can probably be as hot as fire if they wished, but they don't necessarily HAVE to be. I can imagine a Vulpix turning down its heat when it's not fighting, and turning it up when it is. That would make sense as to why water moves make it "unable to battle", not knocked out. That's the phrase they use in the anime...whether it means the Pokemon isn't knocked out but can no longer use moves or not. xD