Regular phasers can drill through a planet's crust. Photon torpedoes make nukes look like firecrackers. A little bit of armor for a few seconds isn't going to matter much. Heck, it's the structural integrity field that keeps ships together much more than the hull itself, no matter the material.
. If I'm going to be convinced that the war timeline is radically different I need to understand how everything but the Enterprise is changed so much.
Guinan. All sorts of timey-wimey stuff seems to swirl around her. (In one of the books they say it's because of the Nexus, but that's just a book.)