Disclaimer: I play on a lower difficulty level. If you're playing on a higher difficulty level, consult other experts.
Go ahead and accept them!
Yes, you'll take a hit on your rate of growth of diplo favor. Eventually, you can grow out of that. Build expansion cities on the former AI lands. Use envoys to become suzerain of some city states, like Hattusa. They're located in decent places, for placing districts. Use them as building blocks for your empire.
In the world congress, you can always get one vote for free... even if you have zero diplo favor. At turn 127, you won't have many super-important WC votes for a while anyway. If the AI cities have rebelled, and you accept them, the AI are defeated. They can't call for a military emergency against you, if those are their last citiies. Unless you have your heart set on a non-violent victory, go ahead and swallow them up.