I'm for the Empire but I hate the Thalmor. So what I am wondering is, will killing Thalmor soldiers hinder my plans to become a Imperial soldier? Will you get a bounty if you kill them? Will attacking "Northwatch Keep" make it impossible or harder to join the Imperial army and will it give me a bounty?

Right now I'm doing the "Missing in Action" quest and since I don't seem to be able to do it peacefully I was thinking of fighting myself through Northwatch Keep but I would like to now what happens if I do.

Attacking people who aren't hostile is always a crime.

Just leave no witnesses. Or get the Thalmor to attack you first by saying you worship Talos.

seeing as how thalmor are usually just with other thalmor i see no reason to leave any witnesses.

So as long as I kill them all or make them attack me first there will be no problem? There is no magical way that people know what I did like sometimes in Oblivion?
And I'm guessing the prosoners won't say anything if I kill there captors?

I'm not sure about prisoners. The first time I tried attacking first I got a bounty. I don't know if it's because I was too close to a city and a guard saw me or if the prisoner reported me.

I've only told them that I worshiped Talos since then.

Ah, OK. Ill try. I hope not leaving any witnessess will work on "Northwatch Keep".

1 out of the 9 times I've encountered them they attacked me on sight. The other 8 they never saw me.

I keep hearing about these people, are they the mean elfs that you see strolling around sometimes. I think I killed two of them but did'nt really pay attention to what they said. I got close to them for to long and they attacked.

Killing Thalmor is a service to humanity. Seriously, I would forgive your crimes if I saw you killing Thalmor.

The Thalmor are a nasty group. Always waiting for your character to look at them the wrong way. I was attacked by a group of three on a road near Whiterun after I ran up next to the prisoner, weapons sheathed. I think they are against any free worshipping people. And i do not know how influential they are in the game. Next time I see a group, they're dead.

I play an Altmer and I do not approve of the Thalmor.

Killing them in the wild leaves you with decent loot as well.

Yes, they're the nasty, overly self-assertive elves.

I've killed every single thalmor I've seen so far and gotten away with it. The three groups I killed were:

1) Random wanderers asked if I worshiped Talos. I told them I could worship what I wanted and they attacked me in plain sight of another group who were going to a wedding. I never got a bounty because I was the one being attacked.
2) Random wanderers had a prisoner. I found that if I sneak attacked them I got a bounty (is the guy I saved reporting me?), but if I talked to them and got them to attack me, again, I don't get a bounty for just defending myself.
3) There are three thalmor in Markarth's court that want you to get evidence of Talos worship from a really nice guy in town. At around 2-4AM, they'll be alone in a room with a sleeping Legion member and a guard outside will be moving around. Wait for the guard to leave around the corner. If you rapidly kill them with sneak attacks (I used a bow) before the Legion fully gets out of bed and then immediately put away your weapon, the guards will forgive you and not attack, plus you'll have no bounty for it. I killed all three and ate the leader's corpse (Namira's Ring).

That sounds like plain Altmer (High-Elves).

If the Thalmor attack first there's no problem, just cut them down. Whilst the Empire supports them it's more because they have to, it's not like the Empire LIKES the Thalmor.

But in "Northwatch Keep" they attack because you tresspass. Or does it not count?

Kill The Thalmors. During the conversation with the rear guard, he said they basicly do whatever they want....so i did whatever i wanted as well, the prisoner didnt seem to mind me freeing him either. But come on bro, sharing in the spoils of the items? my kills, my stuff.

I sniped a lookout and when they came out I just mopped the place up with my sword.

I actually left a few guys alive in the fort. After I picked up the prisoner I used a shout to see life forces. I didn't feel like fighting and trying to keep this unarmored follower alive so I just left the way I came in.

I never got a bounty.