He could call on his guards since they probably regrouped outside the city and then joined in on the second assault...
You're not looking at the issue based on what facts we know, you're looking at it with the intent to turn Ulfric into the bad guy.
Actually I'm not. Honestly. I don't think Ulfric is a bad person, which is why this seems out of character. I just can't reconcile the fact that Ulfric's men were in the majority. You're missing the logical fact that Ingmund had too few men, if any, left. His entire regime was dissolved, his former army was no longer a coherant force. You can't change that in a few days. Ulfric had the only coherant army at the time. Thats why I can't logically say that he didnt play a part in this. Do you see where I'm coming from at least? I know Ulfric is a popular character, and we dont want to think of him as doing wrong, but it's not impossible for him to have a dark past, especially after all he went through.
Edit: And I'm not assuming this about Ingmund's army either. When a government gets taken over, its instituions are dissolved or replaced. Any soldiers left would have either fled, hid, be killed, or just given up (We see in-game that the guards are more loyal to the silver-bloods than the jarl anyway). With a those factors, how many guards do you think were left?Ulfric was the only one with a real army capable of doing these things, or at least stopping others from getting in the jarl's way while his own men did it.