Now that I have looked around for mods, I found out that the Age of Discovery II Mod is doing a pretty good job with this "flaw". What they did was simple, they put a restriction of 20 turns before a player can declare war.
Makes a lot of sense, taticaly and historicaly. In the begining the colonizers had to behave more accordingly to the master nation, meaning that they wouldn be so independant as to declare war in the first years of colonization. Afer twenty turns the AI gets a hold of it and start protecting some of the colonies, making it dificult to start a war later on.
Great Job, I only play AoD II. They even added a pirate nation to spice things up. Its incredible.