what is the general feeling about doing the last dark brotherhood quest if you sided with the imperials during the civil war?

Gameplay wise, no conflict at all. The only conflict is with with the player's conscience (though if you've gotten this far you probably don't have one to be concerned about it in the first place)

I'm referring to someone playing through the civil war on the imperial side but accepting the quest. Then again i could see that as a contract being a contract. Just seems odd if played in a particular way.

From a roleplaying perspective I have problems with a loyal Imperial soldier completing the final quest in the Dark Brotherhood. I can think of a few valid reasons off hand but they would be stretches for me - possible but rather unlikely circumstances that would justify such a path for a character. Still, every character is different so maybe yours is one who is the exception to this viewpoint.

Gameplay wise, as said there are no problems at all. Yay for logical quest consequences and interactions.

I have a problem with it. But my characters might not.

To be completely honest, iirc majority of people you assassinate are A-holes who deserve it, to begin with.

I have only done this once, and it was with a Dunmer who joined the Imperial side just to get to kill Ulfric. He had issues with the Empire, too.

Also, don't forget that Emperor =/= Empire. You may support a change of leadership to strengthen your chosen side.

Me, too. I haven't met the right character for Skyrim's dark brotherhood yet, so I haven't done it (did destroy it a few times.) It took me several years before I did Oblivion's DB quest line, too, but when I finally had the right character for it, I loved it.

Ever since I read a post somewhere that suggested the emperor made the call on himself, so he would become a martyr and it'd be easier to find support for a 2nd great war, I do both questlines without a problem.

If you look at the big picture (thalmor endgame of unmaking creation), you'd do everything you can to prevent that. For me it's the reason to join the legion, and also to assassinate the emperor.

I find it hard to separate my characters from myself. I guess I'm not good at roleplay. :/