Mainly no, a little yes.
No, all PCs belong to the Pathfinder society, its the easiest way to have everyone in the same setting and have them need to go on these missions, nobody wants an organised play campaign were the GM has to entice the players to play the scenario.
The little yes is that if you dislike being an "employee" so much (although its more like a guild with some guild-leaders really) then you can always GM. You get to be the "Employer", the NPCs and the bad guys!
Another thing though is you can just change your point of view. Yes there are those within the society who are effectively just employees, but everything comes down to how you write your character. You can decide that your character is a relic hunting mage who just finds that being part of the society gives him access to a large amount of resources, information and a few heavies to ensure he doesnt have to do any heavy lifting. And if the price of this is that he has to go on the occassional "mission" (ugh) well then at least he can make the most of it and try and make some connections, find some relics etc.
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If you don't like being an employee you'd be in good company. The effects of being a pathfinder are usually pretty minimal after someone tells you "Go somewhere and do this, try no to die"
The factions open up a wide variety of excuses for the character to be in the society.
Silver crusade: ONWAARRRRD! Pathfinders run into a lot of icky, nasty things to be smited and they're good at smiting.
Scarzini: They cover your travel expenses so you can make people an offer they can't refuse, let you travel in the company of allies armed to the teeth in case they refuse anyway, and give you an excuse to leave town just ahead of that rash of fires that suddenly plagued certain businesses.
Qadirian: Cover your travel expenses and lend an air of academia to what would otherwise be a boring bit of trade negotation
Osirion (soon to be scarab sages): Lends a bit of academia to what would otherwise be rank tomb robbing.
Taldor: For Aroden and country!
Andoran: Fight the power! free the slaves!
Different characters can have different level of ties to the society. My fake rogue druid is a society fanboy and grew up reading the chronicles and still sleeps with them under his pillow. My gnome cleric literally just saw a group of people gathering for an adventure and fell into line. He's a cleric of the lantern king, so he thought the lantern lodge was an extension of his cult.
If you describe your character a bit I'm sure there's some way to make them fit.
If you describe your character a bit I'm sure there's some way to make them fit.
Echo this, shoot your character idea, twud be fun to see what ideas people throw at you for a way to fit into the society.
EDIT: Specifically if you could mention what your ideas are briefly for:
Their background
Their personality
Their motivations
Their Desires
Their Hates
By no means do you need to give all of these, but if you can give some it will give us a good idea of the type of character you're looking to build.