I'm running this beta, with the hotfix I think (2-9-4b) and I'm still getting issues with the city-states. No embassies popping up everywhere, but you can still improve a city-states resources multiple times and the improvement is a great person tile improvement instead.
I've seen holy sites and citadels specifically pop up when using the 'improve resource' option.
Also,
@HeathcliffWarriors I wanted to mention I received a 'it's a pity no-one has wiped you out yet' message from Attila - probably because I just settled near him and refused not to do it again (his attitude is hostile currently). I forgot to take a screenshot, but I can at least say it does still happen. Personally I don't mind these, because it means I can goad him into war if I want to.