Here's the thing about the two factions of Brink. Each one is both good and bad.
Security is good because they stand for law and order, and are out to protect the citizen's of The Ark from Resistance attacks. They legitimately believe that The Ark is the last place on Earth where humans live and they want to protect it from those who would lead it to ruin. They're also bad because they're restricting people to The Ark when they could all be leaving The Ark to find Survivors, and they're making the Guests and members of Resistance suffer without supplies.
On the opposite side of things, Resistance is good because they're fighting the oppression caused by Security forcing them to stay on The Ark. Security is holding food and drinking water for themselves, the founders and the original Ark citizens, leaving none for the Guests (who formed Resistance). They also want to find survivors outside of The Ark so that they can help each other return life on the planet to normalcy. Resistance is also bad because they're resorting to terrorist tactics to end Security's oppression, and they don't care which citizens of The Ark are harmed.
Which faction is good and which faction is bad is all based on player perspective. If you want Resistance to be good and Security to be bad, then they are. If you want Security to be good and Resistance to be bad, then you can think that way too. You have complete control to decide which faction is pure and which is corrupt.
It's safe to say that neither the Security ending nor the Resistance ending are canon (canon means they don't happen officially). The reason that neither faction's ending actually happens is because we have this freedom to decide which side to play as and which side is good or bad. If one happens, the other can't happen, and vice-versa. Since they conflict with each other, neither can happen. Unless Bethesda or Splash Damage officially states which side is good, which is bad and which ending officially happens, it's safe to say Resistance didn't actually do what they did in their ending (avoiding spoilers).
Ya what he said Chen was bluffing his men took it seriously Chen didn't think the founder would risk the chance of it all falling apart but after beating the whole campaign it does seem like the resistance is more misguided than security.
The problem with that is, that took place in the What-If levels in the Resistance campaign. The What-Of levels don't actually happen. That reactor being taken down doesn't actually happen. That's what What-If means. It means if something happens --this-- way instead of the way it actually turned out, this is what it would have looked like. So the reactor never went offline by the Resistance.