Well the Hunter and Scout combat should already be the same as the Bandit when they are Profession Hunter or Scout as those professions have a combat of 2. Scouts, Hunters, and Workers should all return back to a nearby city after being defeated by a Bandit. Now, if you attack a Bandit then you attack at your own risk, if the unit dies it dies. Do your Scouts and Hunters actually fight the Bandit or do they just show up dead?
However, I just looked at the code and Animals/Bandits could spawn right on top of a scout. Seems like and odd chance of this but it may can happen. I'll look into this.
Edit: The code actually checks to see if any humans can see the spot before it spawns a unit so they should not be spawning right on top of human controlled units.
@Kailric - I'm not precisely sure what's causing the deaths. It only happens when I have the Hunter & Scout on auto-explore, and every time I do that, they get killed. The message on the screen is always that they died and it is at the end of the turn just as I hit enter and the AI players take their turn, so I know it's happening while they're defending with all moves exhausted. I have the game options set to quick combat, because the zoom to combat causes the game to bog down and eventually crash, so I'm not seeing the combat.
This may be something inherited from vanilla, because scouts in vanilla may as well be made of glass the way they die if you look at them too hard. I'm thinking it relates to the units being mounted. I know dragoons in vanilla do not get defensive bonuses, and I'm also pretty sure that they don't get the benefit of defensive bonuses even when they have promotions that give them defensive bonuses for hills or forests or whatever.
I wonder if this is also true of Scouts/Hunters.
Anyway, it's happened so often that I have stopped using auto-explore.
Which brings up the next issue. I had a hunter parked on top of a mountain as a sentry and a deer passed directly by the unit, but the unit never activated. I watched to see what would happen and the same deer passed him twice, then a bear. The unit only broke out of sentry and became activated when the bear attacked him (although, to be honest, it looked more like the bear randomly drifted into the same square as the unit).
I have seen the same thing happen in Civ4Col vanilla with hostile natives and in Civ4 with animals/barbarians, so I don't think this is something you've done wrong, but some kind of systemic issue in the core coding of the AI created by Firaxis, most likely related to known memory issues on 32-bit systems.
At the moment the game has be designed to work with the King/Pope scenario all other configurations are unsupported. Even the Caliph scenario would not work as historically accurate as they did not impose Censures. We will have to added new scenarios one at a time and test each and add historical factors and events that would have happened. Some scenarios would be:
King/Pop (which we have)
Lord/King (which could work much like vanilla)
King/Caliph (not sure what the king would be called)
and Independent (no king or pope)
Also, we would have to factor in Economy Type and Starting Locations
Starting Locations are Water (on a ship), Land, or Advanced where you have points to spend)
A couple Economy Types:
The Trade Routes (we'll say this is what we have now in M:C)
The Europe Type (as in Vanilla, this could work for a Colonization effort by Vikings returning to Motherland to sell their booty and have to deal with a Viking King as in the History Channel series "The Vikings". This could also work for Muslim colonization Civs)
Now, my question is what type do you want to work on first as we would need to handle each in turn?
But to add a civ of the Landstart, Trade Route, King/Pope type just follow the examples given.
The issue with history is that most of the guys who make the pages didn't answer to anyone, but the Civ4Col core is designed around a build up to revolution and independence... which doesn't have a 100% historical relevance even in the colonial Americas. It's that damned Amero-centrism they built into the core. In the case of the Kievan Rus, those guys answered to no one. They were on kissing terms with the Byzantine Emperor, but that's as far as it went. Then they had a few centuries of kissing Mongol butt...
The Republic of Novgorod though, they had something very similar to old Scandinavian kingship, which wasn't much like medieval European kingship. Their princes were more or less guys hired by the ruling committee to fight a war, then they were sent home to grow flax and shave sheep, or whatever. So in a vague way, a prince of Novgorod might answer to a higher authority, but most definitely not in the Civ4Col method. The closest they came to a Civ4Col revolution was when they broke away from the domination of the Grand Duchy of Muskovy (which had seized control of the region with Mongol aid). So in a "scenario" sort of way, the Novgorodski could be made to fit.
The Kievan Rus and the Muscovites are easier, I would set up answerable to the Mongols with a build up to a revolution.
But the Abyssinians... They just don't fit the Civ4Col model at all. I think they're historically important to the M:C setting because of the Prester John myth, but how I would go about setting them up as a playable civ, I just don't have any solid ideas. To me, they seem the ideal "play to survive" civ, but they controled a portion of the Red Sea and had access to the Spice Route and were one of the major suppliers of the Perfume/Incense route (Frankincense and Myrrh baby). Also, they were most probably the originators of coffee-drinking, so adding them creates a historical reason to add a new resource.
Lords in the Caliphate were called a lot of different titles, but by the early Ottoman period, Governors of large provinces were called
Walis,
Sanjakbeys, or
Mutesarrifs, and lesser administrators/petty lords were
Kaymakams,
Timarlis, or
Beys. If they were one of the Slavic vassal lords, the term
Voivode or
Vadja was generally used.
On a related note, I finally have the City ArtStyles figured out (thank you Orlanth and melcher kürzer). Now, I am thinking that I need to learn more about the Unit ArtStyle thing, because I seriously want more flavors of native >_<
view it now for the low-low price of 1 Plate Armor and 10 Ale! 
Or, could also start a game in the Early Middle Ages where several small nations are already in existence and have to expand & compete with each other. (likely more historical than a single colonist arriving.)
This would work for certain Civs or even the ones I have now would mostly fit that scenario as well. The nobles demands and Tithe rate could be there to both lower the players over all profit as the game progress thus increasing the players need to quickly build his army before the enemy arrives.
