Yeah, as much as Gene did creating the franchise, it noticeably got better once he was out of the day to day parts of it. TNG saw a rise in quality, DS9 would've never happened at all under him. Idealism and hope for a better future is good, but when is starts overriding common sense and believability it gets a bit silly.
To the episode in question... this was easily Garak's crowning moment. He utterly played -everyone- from Sisko to the entire Romulan Empire. I liked the narrative approach too. Not only was Sisko doing these things, but he was believably justifying them that you could see a good man making difficult decisions and doing bad things for the greater good.
I would've loved it if somehow Dukat got a hold of that log entry and declared they weren't so different after all!