The Vengeance is larger than Enterprise-E but is more primitive, even if advanced fro its time. Consider...
The Enterprise-E can modulate its shields and presumably in the wake of Voyager's return has much improved armor. Even the Enterprise-D demonstrated great versatility in its technology, including a much greater transporter range and an ability to almost re-configure a planet's atmosphere! This vessel is designed to take on Borg cubes and survive, as well as Dominion capital ships and the topline warships of the Klingon and Romulan empires a century later than that of the Vengeance.
Keep in mind also the Vengeance didn't manage to destroy the original Enterprise. Even with surprise on its side! Yet that very same Enterprise managed to kill every single person aboard the Excalibur, while engaging another three Constitution-class cruisers! This was before the refit!
Interestingly (or not, since the show was of course severly limited by it's budget and the technology of the era vs. a modern blockbuster) there was no visible damage to the Excalibur after this killing blow. Perhaps M-5 damaged the inertial dampners and gravity systems, reducing the Excalibur crew to 1mm-thick paste on the rear bulkheads? A lucky or ultra-precise shot, rather than a show of brute force as we saw with Vengeance vs. Enterprise.