Yeah, it's easy to miss that detail at the moment since it's buried in the tooltip for scythes. I'll think about how to make it more clear!
Thematically it is because the enemy is "just the right amount of dead" to make into a zombie. When it comes to design we try to add these mini puzzles to the combat to make it a little more interesting than just "maximize damage at all times". It also makes a very strong mechanic (reaping) just a little bit weaker.
It does add some complexity, though, and the type of feel-bad moments that you experienced are very unfortunate. I like it the way it is but maybe it would have been better to keep the mechanic as simple as possible. Game design is hard :)