See my sig for my definition of "good thalmor".

The Thalmor wish to uncreate the world in some mad scheme to achieve divinity.
That Tiber Septim transcended above their gods by more forward (as opposed to the Thalmor's more backward) methods offends them. That Tiber was a man even moreso.
I have a feeling that Alduin was just the first threat to reality that the Dragonborn will be putting down. I think that Beth may be doing a "story arc" DLC run a la FONV's involving dealing with the Thalmor menace.
By his/her very nature, the Dragonborn is the greatest threat to their plans they will ever know. They just don't know it yet.

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