RTF is a global modification that replaces all towns in the game.

How can good and bad guys coexist under the command of one player?

And how can red and white troops of the empire coexist under the command of one player? Besides, "NOT good guys" are not primarily villains, but mercenaries – you pay them, and they work for you; the point is that they don't care who pays and what orders they are given.

Added 4 minutes later

They don't seem to fit the Heroes theme...

In theory, Duncan could have survived:D

Added 2 minutes later
And it's not very practical to take heroes from the same city.

What does it mean they don't fit? Any character can play their role, and as they say, "heroes are not born..."
I don't see anything that strictly ties them to a specific city.
In general, I am in favor of using lore characters (by the way, something might be useful for NHF as well)