What exactly makes the guards levy the crime of Assault at you even if you make a Good Thalmor right in front of them?

Because they're non-hostile agents of a sovereign state with whom the Empire aren't at war?

Even so, they still must DIE!

Nono, I meant the technical aspects, what's going on with game actor behavior. What prevents the guards from going "MURDER!" at you and just go "ASSAULT!"

And you must have a pretty strict definition of "hostile". They're quite hostile... just not openly so. I prefer to drag that hostility out in to the open, where their cloak and dagger hostility will not avail them.

I've never had an assault fine from killing thalmor. Just provoke them with dialogue about worshipping Talos and make them attack first. The guards can't blame a Dovahkiin for defending himself.

As for why, the Thalmor are probably set to a faction that when attacked/killed the guards see it as an assault.

What is really sad is that if you see a group of soldiers from both factions of the civil war fighting each other and you help your selected side, once the fight is over you will be attacked by your allies for assaulting the other side members.