It's an intriguing idea. I love Deus Ex, and played it right through several times. But...
DX doesn't really give you a choice of which side to join. You can choose your equipment, and your route through each mission, but the underlying story is firmly on rails. And for a good reason.
Imagine, mission 1, you get directed to bust some smugglers, you go to the house, find the incriminating documents implicating the government. Mission 2 you get sent to a bar where the guerrillas are reputed to hang out. You use action menus to talk to some folk. Do you arrest them or ask to join? Mission 3 - there have to be a couple of these. Mission 3a - as a member of the resistance, you steal guns from the police station. OR Mission 3b as a loyal policeman you raid the resistance HQ and arrest / kill as many as possible. Either way the mission designer has to make 2 missions, but the player only gets to play 1. The more choices the campaign introduces, the worse it gets. Eventually the player gets to mission 7 - the final battle, but by now it's mission 7e, and the designer has had to build 19 missions to get you there, followed by at least 4 ending movies (res/police win/lose).
Unless the missions are so good that a player will go straight back to the beginning to try it a different way, most of the designer's work will be wasted. :'(