How do I prevent rats from eating a corpse that I left unattended? Also, is this a bad thing?

Solution 1:

Unconscious bodies are vulnerable to being eaten by rats. You can store them in garbage bins to make them completely safe. The same holds true of corpses. There is also an ability that turns corpses you kill (level 1: stealth kills only, level 2, both) to ash, making it a non issue.

A kill is a kill where Chaos levels are concerned. Tucking the bodies away/disposing of them helps prevent you being detected in mission, but if they are actual corpses they're going to contribute to potential chaos level increase regardless.

Solution 2:

If there's no garbage bins around, try putting the bodies out of reach of rats that might spawn - small tables are probably best so that the rats would be unlikely to spawn on the small surface area of the table. If you're trying not to kill many people at all, rats will be quite rare anyway.