The charector arcs in the show are complex, especially for the early 90s. Sisko is largely an honorable man, but the nature of the roles he assumes strain him, force him in difficult directions.

The marquies in a lot of ways are personal to him. A dear friend defects to them early, and then he gets rolled later by others he trusts. He basically has direct bad blood with them.

Some of the other choices he makes? Fucked up, but to the shows credit, they lean into it and dont pretend hes the good guy when they happen.