Let's See - what did Sisko allow Garak do to the Romulan Ambassador (who knew the Federation evidence had been faked) so that the Romulans would enter the war on the Fed side (in DS9 - "In The Pale Moonlight")?
And what actions did Section 31 take prior to and during the Fed/Dominion War - all in the name of preserving the holier than thou Federation?
Well, did you know that DS9 wasn't perfect? In fact, it was pretty much loathed by a bunch of Trekkies and is still always the "underground" choice. Those specific episodes are one of the main reason why, they rubbed a lot of people the wrong way.
For me personally, it was Sisko firing biological weapon on a Maquis-colony - families, children and all - which was complete character assasination for me ("For the uniform"). It was a plot ploint for this episode. But
after that, this fucker should have been trialed and jailed like any other war criminal deserves. Or at least the writers needed to admit they have a
villain protagonist, a bad guy, like
House of Cards or
Death Note have, as their main character. But they chickened out. They still pretended he is "deep down a good guy". He got a slap on the wrist, and everything was fine again.
For actual use of WMDs! And later
murder! Which is a shame. Because, apart from that, Sisko was one of the best written , well-rounded characters Trek produced. But a war criminal can
never win the contest for "best Captain" or even "admired hero".
I fear Discovery runs into a lot of the issues many people had with DS9 - too much focus on WWII
IN SPACE!!!, 'shady' characers, a grim'n'gritty tone, and war crimes being part of 'character building'. Now, I'm not opposed to tackling
any of those issues. I love movies like
Apocalypse Now, or the new
Battlestar Galactica. It just does not belong to Trek, because Trek never completely pulls through with it, and always wants our heroes to be
both people doing questionable things
and still heroes to look up to. That doesn't work. That's the one thing that didn't work on DS9, and made the arguibly best character written Trek show one of the least fan favourite ones.