It really seems like the Federation would've put all their cards on the table when they were that close to losing. Genesis device, thalaron radiation, sub-space weapons.
I imagine the Federation that fought a twenty-year war with the Klingons was on the whole a darker, scarier civilization.
Yup. I mean, in the REGULAR timeline, look at what the Federation did to beat the Dominion. They tricked the Romulans into being their allies so they could win the war. There's no telling the horrible (but perhaps necessary) things they would've tried in the alternate timeline with the war against the Klingons.