1) who are the Thalmor and why are they sided with the empire even though they want to destroy them, is it because of their contract?
The Thalmor is a militaristic group of the third Aldmeri Dominion, mostly composed of High Elves and intent on establishing racial superiority of Elves (Mer) over Men. It is indeed the White-Gold Concordat that for the moment keeps a kind of truce between the Empire and the Dominion, after both sides suffered huge losses during the Great War. Neither side likes the other but for now they prefer truce over an open conflict.
2) is ulfric secretly with the thalmor? If I join the storm cloaks since I am a high elf will I be descriminated against?
Ulfric is most definitely
not secretly with the Thalmor; he and his lieutenant, Galmar, hate the Thalmor with a burning passion.
Despite the conflict, the player actually won't be discriminated by others no matter your race. You will possibly get a few unfriendly or snotty comments but that's about it.
3) whoever I join can I still kill the thalmor regardless?
No, only when you join the Stormcloaks. When you side with the Empire you have to respect the White-Gold Concordat, at least in public. However, if you are sufficiently well trained in sneaking, you can try to take the Thalmor out without anyone detecting you (quite hard within cities). You can also kill any Thalmor you come across on the road outside cities, as long as there are no witnesses.
4) who in the literal heck should I join
For the gameplay, it literally makes no difference: the quests are very similar in both factions. The only difference is that depending on which faction you side with, the Jarls (and their entourage) of the cities held by the enemy will change when you conquer them. So if there is a Jarl you like specifically, be sure to check his allegiance.
You can always wear the armour you want but if you want to stick to the role-playing and wear the faction-specific armour, be sure to note that Stormcloak armour is light, while Imperials have both light and heavy armour (higher imperial officers tend to wear heavy armour).
As for my personal opinion, I used to be Stormcloak since I usually play as a Nord, but I tried both questlines and ended up disliking both Ulfric and Tullius. However, I have a great respect for Legate Rikke and her view on the conflict. Before making your decision, be sure to speak to Ulfric and Galmar (Stormcloaks), and Tullius and Rikke (Imperials).
If you need more detailed informations you can always consult the lore and game-specific pages of the Unofficial Elder Scrolls Pages - be warned that the site contains a lot of information, which means watch out for spoilers! So maybe start with the lore pages first.
Of course I'm always happy to answer any other question you may have about Skyrim
