I would like to replace the original races, basically have rid of the non Mesogea races and rename the remaining ones. What is the safest way to do this? Would people still be able to port their old characters into the Mesogea world? Would it create errors for characters already created with vanilla races etc?

You would have to change the races of all NPCs that use the vanilla races. ...Maybe that can be done dynamically with OBSE, but why not just overwrite the vanilla races?

I haven't touched the cs in a year or two, but why delete them, can't you just uncheck the playable checkmark. Then you just make a copy of the races you want to keep and rename them. I dunno how it will affect importing races though, but its a total conversion so why would people import characters.

I like the unchecking idea, that would be the simplest way ahead and still allow people to enter the world with their old characters. The mod will be a complete overhaul yes, however until its in a totally playable state with some quests etc, people will need to use their characters to go visit and look around.