That's what I was trying to accomplish and up until The Battle for Whiterun (Imperial side), it worked. However, the quest ID for this quest is exactly the same as the ID for the Stormcloak Battle of Whiterun. So I typed in the ID, and when trying to skip the quest by the bat command, I got the following message:
COMPLETED: BATTLE FOR [...]
The word Whiterun didn't show up. I tried to continue with the next quest but then I only got the COMPLETED: [...] message, this time the name of the quest didn't even show up.