as it stands, the interface doesn't warn you that refusing to promise is for the rest of the game, and the interface does not indicate how many turns left you have until a promise expires (if you accept it).
Yes, the interface does not indicate that, as it does not tell you or just plainly misleads you about great many of other things. Honestly, it is the worst UI in the entire franchise and one of the worst among all other strategy games.
To get back to the conversion business though, you can convert civs that have not founded their own religion without any penalties. Kongo is a special case in that they can't found a religion, but they can get apostles of other religions that have been spread to them and they can and will attack your religious units and can kill them, if you're not careful, reducing or removing the presence of your religion in his lands, and that will piss him off. You see - he attacks your missionaries and is also upset that you fail to spread your religion to him and satisfy his agenda. The man's crazy as a bat
If a civ has founded a religion, it will not like the spread of other religions, and you will generate grievances promise or no promise, only some amounts will differ. If you convert and accumulate grievances faster than they decay, eventually you'll get denounced. Other civs will also see that you cause grievances and start showing negative diplo modifiers against you because of that (caused grievances to others), leading to even more denunciations. You may even face a dog-pile war against you in the end.
Negative diplo situation can be mitigated though or even negated. Become friends with the world before you begin. Achieve as much Declarations of Friendship as you can and start converting. You will still pick up huge amounts of grievances, which will convert into huge negative diplo modifiers, but once locked into a friendship, this status does not change for entire length of 30 turns. Just don't let them off and renew all DoFs upon expiry, on the same turn. They will agree despite ovewhelming red negative diplo modifiers. Miss a turn and you may be in trouble. But while friends or even allies (except religious allies), you can continue to convert them in peace, ignoring all the grievances.