I think you're reading into the description too litterally. While it certainly wouldn't directly contradict what's there to have the Sobek in action against remaining Great War Shivan forces it does say that it 'began' it's design in the days after Vasuda's destruction. I'd also interpret 'days' in a more metaphorical sense. Directly after Vasuda's destruction and even up to the end of the war there wouldn't have been much, if any in the way of new designs. You concentrate on building what you know works.
Also, it's design and testing would most likely take years and I'd put money on the Sobek class being designed around beam cannon's considering the seemingly inherent problems with integrating beams into pre-Great War designs.
Plus, while making a good story, once billions/trillions have been pumped into actually designing a ship it's genenrally not necessary for the class namesake to have a glorious and noble self-sacrificed end to ensure that the design is used to build countless others. It just needs to work resonably well.
Look at the Aten. That didn't even do that and still got churned out.
Edit: But I suppose for the sake of story you could have the very early testbed 'Sobek' design, armed with minimal defenses as it's still in it's engine testing phase, soak up a load of bomber attacks for a science/civilian outpost/colony before having no choice but to ram a capship, as starlord suggested.
Wasn't the Eva the only Daemon with the Shivan fleet? A cruiser seems a small ramming target alright though.