Paladin Spell Casting is easily, and sensibly to my mind, replaced by a feat at each level the class would gain a new spell level.
Extra abilites tied to deities also seem like a good idea.
Thematically I think replacing the Turn Undead ability with a Favored Enemy mechanic, or maybe even a kind of Band of Brothers thing where Templar's within X feet of each other recieve X bonus, increasing at certain levels. Something very similar to Turning, but slightly different would be an Exorcism or Turn Outsider ability. I like this for the Paladin and it might work for your Templar.
You said in your original post that the setting was inspired by european dark ages, thus my reasoning that your Templar/Knight class should be the same. When you make statements like: "They aren't noble, they aren't mounted, they aren't leaders and they don't go to war. They usually either go to quests for their church or stand and defend the temples.
That's why I thought they should be different classes." you are basically telling us that it IS NOT like the European Dark Ages. The assumptions you are working on aren't clear.
Same with comments like: "The Archer must not be a Fighter with archery feats, otherwise there would not be any reason for it as a separate class." make no sense to me. You are begging the question. You assume that there must be an Archer class but that statement doesn't tell us why you think so, nor why the fighter class needs to be divided into 3 classes, when perhaps individualized sets of fighter feats might work.
I am not trying to be difficult or attack you or your posts. I simply find that in most cases one will not achieve anything without a clearly defined goal. In developing a set of classes for a campaign world that goal must be something like : I want this campaign world to be X." Where X is some period of history (however modified), a genre from fiction, or a particular novel, comic, TV show, or movie you are trying to emulate.
So,What's the goal? Is it a fantasy version of early dark ages europe? If so then everything needs to work back to that point to support that idea.
If change is the only goal then change is all that happens. Usually not unified or with any real purpose.