I'm sure they can, except when all your soldiers are generally tradesmen who kept your Holds productive, you kind of need them to return to their work. Fine example would be the lumber mill in Eastmarch which is not operating due to all the able bodied men off fighting the war, not only are you losing out on access to wood to repair your cities, houses and various items, you're also losing out on creating more arrows, shields and wagons for the war.
Comes back to the point of poor management. The Stormcloaks can rant and rave about honor and fighting, but that alone doesn't win wars. Nor does it make them better suited at ruling all of Skyrim.
Besides the Legion you still have to contend with the out of control bandits, large numbers of Forsworn spreading to raid several spots in other Holds and the Falmer starting to surface. You can't even handle Windhelm anymore, but keep on spreading to other Holds. In the end you'll not only bring down the East, but the West with you.
So the reason Windhelm is weak, undermanned and has unrest which could lead to revolt in a quarter of the city is because "Empire is giving Ulfric power that he needs"? Damn, have all the power you want.
Refuses? The Empire fought a major destructive war that cost lives and extensive resources.
And Ulfric did exactly what was needed to contribute to the almost complete genocide of every living being on Nirn...
The issues with the Thalmor Justiciars are recent. They're using the rebellion to step up their game, though they are indirectly aiding you Stormcloaks.
Though yes, the small handful of Nords that were arrested prior to the rebellion was contributing to the genocide. Cause the thousands who now die over Ulfric's actions in battle, starvation or by out of control bandits don't matter.