Just to clear up any "horrifically bad information" I may be passing on...
The idea that the Protagonist and the Main Character have to be the same person is an outdated concept that stifles writers and obfuscates true meaning in narrative fiction.
As Steven points out, you can combine the two to get the classic "Hero" character that most writers are comfortable with. However, if you want to write something different, something unique and closer to real life, then yes you can split them apart as in the aforementioned "Mockingbird." "Shawshank Redemption" is another great example of a story where the two are split.
Why would you want to differentiate between the two? Because the thematic issues that affect everyone in the story are not the same as those that affect the Main Character personally. In point of fact, it is the differential between these two that actually provides the meaning audiences are looking for. In real life we cannot live both within ourselves and also look outside at ourselves objectively - it is a physical impossibility.
This is why stories exist - to provide us with both perspectives and therefore give us the meaning we so often crave, yet can't find in real life.
The Main Character provides the inner viewpoint, the Protagonist (prime mover of the plot), Antagonist, and so on provide that external 3rd person view.
The problem you are having with "Star Wars" is that you haven't identified the true goal of the story. Before determining the Protagonist/Antagonist, it helps to figure out what the goal is first.
Everyone thinks the goal of "Star Wars" is to blow up the death star, but this really doesn't come into play until the latter half of the film. The real goal, what everyone is most concerned with or interested in is rebelling against tyranny and oppression. Note that this is not the common kind of goal that most people are comfortable with and I'm sure everyone will jump on me, but when you really think of the concerns and issues present throughout the entire story, this goal of rebelling against tyranny is more accurate than simply "blowing up the Death Star".
With that goal in mind, it becomes clear that Luke is the Protagonist (he wants to fight the empire) whereas the Empire is the Antagonist (they want to prevent him and his buddies).
I have written two articles that explain this is more detail. Both contain slides that I use in my presentations given while teaching Story Development at the California Institute of the Arts:
Archetypes That Make Sense
Character Motivation Defined
The latter also has a 10-minute video explaining in great detail the character archetypes present in "Star Wars".
It has been awhile since I've seen "Thelma and Louise", but if I remember correctly, Thelma (Geena Davis) is the Protagonist while Louise (Susan Sarandon) is the Main Character. I'm not sure if this is the same kind of dynamic you have in your own story, but it certainly sounds like it.
I hope this helps. If you have any questions about anything feel free to write to me at http://storyfanatic.com/contact
and I'll try to help you out as best I can.
The important thing to remember is to write first and only refer to this stuff when you are stuck or if you feel like what you have in mind isn't what everyone else is telling you. Your intuition should always rule.