Play one campaign. Then the other. The people you saw in the a opening scenes of the other campaign, talking about making breakfest for their kids, or worried about their family? Those are the people you're now gunning down.
In one cutscene, a Resistance member frets that his brother is on Security, and a fellow Resistance member warns him he can't hesitate to shoot Security, since they won't hesitate to shoot him.
Even worse is playing the Resistance campaign and then the Security campaign. In the Resistance campaign, the main goal is to leave the Ark and make contact with the outside world. In the Security campaign, the main goal is to stop that from happening because the Founders already sent a group into the outside world and they were slaughtered to the last man. The world is exactly what Security claims it is, and the Resistance is effectively crippling the Ark to embark on a hopeless suicide mission.
Later changed in the Agents of Change DLC, where it's revealed that the escaped resistance members actually did find civilization outside the ark, revealing what Mokoena said to either be a lie or an uninformed statement.
It's not just the Resistance who end up on the wrong end of this, though. Fighting for Security to prevent the Resistance from escaping and bringing doom upon your heads seems like a noble goal, no? Then you read one of Chen's audio logs. The Arkoral is mutating and going sterile. The Ark, the basket in which you have decided to place all of your eggs, is literally dying, and it's only a matter of time before it crumbles away beneath you.