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So I've joined the Stormcloaks because these Imperial guys kept attacking me. Now Stormcloaks want to attack Whiterun but I like Whiterun. What do I do?

Turns out Whiterun likes Imperials... Hmm..

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You can not continue with the Stormcloak quest. Attacking (Stormcloak) or defending (Imperial) Whiterun are your only options if you want to do the civil war quests.

You shouldn't worry too much about it, though - the impact of these quests is fairly negligible.

You can also run away like a punk after getting your orders at the camp and go straight to Ulfric. He will be annoyed, but the quests will continue as normal (the battle will be won in your absence).

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It's pretty much impossible to choose a side without the battle for Whiterun taking place. Whiterun is the one hold that is completely neutral, so likewise it's a hotly contested battleground between the Stormcloaks and the Empire. Fortunately you don't have to continue the storyline if you don't want to, and as a previous answer says, you can just duck out of the battle as it's taking place. But, everyone will still blame you for it and will still consider you one of the sieging parties.

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