Hi, I decided to take part in the civil war and I am now in the last stage (solitude). I just heard, that for the dark brother hood I will have to assassinate the imperator. I have not yet started Dark brotherhood... Is this still possible if I defeat the imperials?

Yes i'd assume so, they're not going to cut off one questline just because you did another first. Though that would be pretty strange for the Emperor to visit Solitude if the Stormcloaks control it.

Anybody did the quests in this order and can tell me his experience?

push

Yep. The Emporer is still out there on the ship, waiting for you to kill him. It seems inconsistent but it's necessary. It's part of the do what you want when you want to do it philosophies of Skyrim. So feel free to assault Solitiude. But really, the Emperor's ship is getting ready to leave when you kill him so it's not much of stretch to say that he's fleeing Skyrim due to the fall of the Empire.

That I would understand,

...but what about the Vittoria VIcci part? I'm guessing it's still doable, but that would seem really weird.

it all happens as though the stormcloaks werent in control.

What do you mean? Oh... I see what you're saying. Well yeah... But in order to be able to do quests in the order you want to do them and/or stop and then come back to them 20 levels later, it's inevitable that some huge plotholes will develop.

Yeah. It seems weird, but I too would rather have plotholes than game-stoppers or -breakers.

A game-breaker would actually make sense here, but I understand why they wanted to avoid it happening. Really, though, if the Stormcloaks sack the city the Emperor's sole concern should be to GTFO of Dodge ASAP, as the place is now hostile territory.

It'd be nice, though, if they stopped worrying about someone screwing things up in the first place and instead assumed it would happen and designed accordingly. Would be a great use of branching quest lines, for one thing.