If a dead animal is electrified, will it decay?
Environemental factors would degrade it (wind-water etc.).

But from what I know, electricity will follow a certain shortest path inside the body to close the circuit. The rest shouldnt be electrified and bacteria will be alive.

Bacteria are indeed not resistant to high levels of electricity and would die of it. The current would need to traverse the Entirety of the animal to kill every single bacteria which is highly improbable. Leave one alone, it will reproduce fast.

From what I researched, a constant electrical current of the power of an electric line would cook the animal in a short time. The flying fox you saw probably didnt have live current traversing him anymore and died from a quick jolt (this is a guess only). 

Even in the extreme case that 100% of the bacteria would die, the dead animal would be recolonized by bacteria really fast. Even in the wires, wind or animals would carry bacteria. 

Power lines are probably protected from arcing this way through anything that could touch them. Imagine if they werent, trees touching them would burn, shoes you throw and hang on them would be calcinated etc. 

Off-topic: Are you sure he wasn't only sleeping on his improvised power-line hammock ? :P

Sources: 

Conduction of Electrical Current to and Through the Human Body: A Review

Effects of high electric fields on microorganisms I. Killing of bacteria and yeasts