Thank you for the feedback! My intent was indeed to show that this so called "Resistance", may not be the good guys after all, or even the cure for what ails the people. I didn't have time to flesh this out, but my intent with this faction (in the future) is to be satirical and show how they don't really know what they're doing and are in some ways worse than the actual government they're trying to overthrow.
There's a bit of connection to this intent when you find a Wrea-der log next to a dead body, hidden in a room in the Refectory. The woman who calls herself Resistance Alpha is named Jacquie (you only know her name is Jacquie if you scream when talking to her), who is referenced in that Wrea-der log.
The Wrea-der log also references how the security outside his door didn't do much, as the dead person was the person living in the house the Security Watchdog is guarding. If you read the email on the computer you can see he snitched on the ex-resistance guy (John) who's house you now live in, and got John killed.
Jacquie was undercover as his wife, and killed him by locking him in a storage room.
Was this sidestory poorly told? Yep, it was, especially since it's hidden in optional side areas. But of course, it all goes back to being a jam game and me biting more than I could chew!