Capitalizing the first word after a misused comma doesn’t make the sentence any less a comma splice.
Change the comma after clans to a period and fix the spelling of witch. (That’s one doozy of a typo!)
I changed over to more than to make the meaning clearer.
There was a war going on between the witch clans. It had been raging for more than two centuries.
(WordPress’ spell check wants me to change witch to which. It has no explanation for why it thinks this is the correct spelling.)