He's too ethical to join up with a terrorist organization.
Theseus isn't necessarily a "terrorist" if you are working for a police force that is 100% rogue..
I think he saw that the Police had become corrupt and that he had nowhere to turn, but to the very organization that was fighting against the people he had just turned his back on.
HERE ENDS Discussions.. now for theories:
So, I just finished season 2...
The Freelancers are from the future, farther future than 2077... what means Mr. Escher is from the future, he was a "Freelancer," - now this is where it gets slightly shaky.
In 2013, Mr. Escher creates Piron.. in the future, Piron is one of the companies who is a part of the 20 CEOs in the corporate congress. This is also the company that was "hording" food in the future in one of our flash forwards.
If you remember in Kiera's flash forward, her last memory of her son is complaining about the "slop" that they are going to have to eat.. this scene has been shown many times before, and I believe is extremely important to the whole thing.
Food and Drink is becoming sparse in the future - Kiera disappears.. nothing ever changes, Sadtech is ultimately taken over by someone other than Alec, they create super-soldiers who can travel through time.. the first person they recruit?
Kiera Cameron's son of course...
Kiera Cameron -> Mr. Esher -> Alec -> Jason
Mr. Esher is creating Piron in the present, in order to fix the food problems of the future.. in hopes that the food problems will never happen.
Alec of the future also sent back liber8 to stop a dark future as well.. the ultimate bad guys of this show -> the Freelancers, who are only watching out for their own self interest, in order to make sure the dark future (after future Alec is finally gone) ends up truly happening.. it's why they interfered in 2077 AND 2013.. Alec MUST become the person that creates SadTech, else the freelancers never exist in the first place.
Also - I think Alec got his tech for traveling in time, from the Freelancers - very terminators stuff.