I have yet to begin any civil war quests, and have remained neutral to both sides. If I complete the To Kill an Empire quest that Astrid gave me will I still be able to join the Imperials? Seems a little bit weird for a guild quest to basically choose which side of a semi-main quest line to be a part of, which is why I'm asking before going ahead with Astrid's plan.

Yeah, you can. I joined the Legion first, and then completed the quest. So much herpderp.

Yeah I mean. I just really don't like the Ulfric or the Stormcloaks. I just don't really understand why this particular quest is in the game, or at least why there's no option to assassinate either a Stormcloak Leader or an Imperial Leader.

You do if you play the Civil War through to its end as one side or another. Though, tbh, it's not worth much. It should have a massive impact on the game-world, but it really, really doesn't.

i joined the legion and im still going to kill this emperor because hes kind of a [censored], and what the [censored] is he doing in skyrim eating gourmet food while theres a civil war instead of trying to make peace with ulfric, he deserves to die....

Oh, that's good to know for a future endeavor. I haven't started the Civil War at all because I've heard that starting the Civil War while having progressed to a certain point in the main quest will bug out both quests. I'm already beyond what I've heard is the point of no return in the main quest that would trigger this bug, so I'm not touching the Civil War until I finish. Seems like you really have to tip toe around quests in order to avoid breaking things. I guess I could wait on the DB until after finishing the Civil War? But that kind of screws up my whole plan.

This is where the imagination comes in. No Elder Scrolls game has ever taken the time to openly acknowledge what you did in X questline afterwards. A few lines of dialogue maybe, but not much else. That's the one drawback of being able to play after all the important stuff. You have to assume it's in a "bubble of time" where people aren't all knowing about it yet.

And with the Empire in such a delicate position, you can rest assured they'd try and cover up something that big to save face and to not look weak.

I am pretty sure you can let the Emperor live and kill the guy who tasked you with the quest instead.