You're right, she should, um, vaporize. This doesn't happen because, as you said Anime Physics.
Another reason we can consider is that Magcargo probably purposely regulated its own body temperature so that the little girl couldn't get hurt. This makes more sense due to how generally, Pokemon are kind towards humans.
That said, another reason is simply that the girl's power of love shielded her from the heat. (/s)
To be honest, apart from Magcargo purposely lowering the heat, I don't see any scientific reason why the girl didn't turn to Satoshi (lame joke because Satoshi = Ash, please forgive).
One thing I would like to point out is this: A lot of the Pokedex entries are often exaggerated for dramatic effect so it appeals to a wider audience. For a younger kid watching Anime and hearing how cool (or hot), i.e. overwhelmingly overpowered Pokemon really are is a great way for them to appreciate it so much more, and ask for the games to play, increasing sales. That could be why the devs purposely give such dramatic entries.
In fact, by what's written in Magcargo's Dex Entry it should be immune to Water types, but as we know the truth, it suffers from a 4x weakness and is generally weaker than most other Fire types.