the characters that we built and the rapport that we had with each other was amazing
I have to admit, I thought Alok was a pretty interesting character. Sam Richardson was also very charismatic as Quasi, though he didn't have much to do. And Young Garrett was okay, too.
I wouldn't mind seeing any of those characters pop up again, with a better story.
This was never credible, and was never how it was presented in DS9.
Even in "Inquisition", Sloan had two other guys standing next to him, and an entire starship at his disposal. Starfleet Command covered for him at the end - something that was noted by the DS9 senior staff.
In subsequent episodes, Admiral Ross acknowledged their existence, and Bashir worked out what he believed to be the bare minimum number of operatives required to create the morphogenic virus (73).
Later, we saw them working for the United Earth Starfleet in the ENT era.
The only suggestion that it's just "once crazy guy" comes from Koval, who then helps Sloan fake his death and is revealed to be a S31 asset in the very next scene.
So no, that's not really something Discovery changed. People have had to wilfully ignore the DS9 episodes to buy into that theory.