My point is they should not kill them. IRL 1 unit of Spanish conquistadores conquered South America, and another single unit conquered Mexico. In Civ, IV the adequate tech level wouldn't be knights and macemen but warriors and maybe archers.We already have this in Civ4 Terra map; new world tends to be macemen and knights when you arrive. If you only bring a few units, they *will* kill your stuff.
We already have this sometimes in Civ4 continents script and others. Some continents are "good", others are "bad". Good continents are often way ahead of bad continents when they first make contact.
Good and bad continents have an impact on the tech, but it is not as drastic as the differences in techs witnesses IRL (American civs in 1500 were way backwards compared to Europe, which hardly ever happens in Civ).