>>40310498That would be because Pokemon aren't being beheaded. Guillotine isn't literally a guillotine, it's just an ordinary slashing attack.
A lot of hyperbole is used in Pokemon, especially in the Japanese version. Fainting is called "near death" in Japanese, but it's explained that the Pokemon is actually nowhere near close to death and is just too tired to battle. And the anime just refers to it as "unable to battle".
Tl;dr Pokemon battles are a completely safe sport. Pokemon never get killed or seriously hurt in battle.