I at first didn't realize how evil covenant was because I didn't do everything in quest leading up to the confrontation with Dr. Montgomery
The first time I played I botched the playthrough of the quest where I'm supposed to look for clues, I couldn't find all of them so I just skipped ahead to the compound across the river.
I met the cold hearted scientist who ran the compound, Patricia Montgomery. Of course I chose to take her out because she's an evil witch
What I didn't expect was that the entire town of covenant became hostile, I at first assumed that I aggro'd them by picking a lock or stealing an item while scouring the area and that it had nothing to do with me wiping out Patricia and saving Stockton's daughter but again, I never completed the whole quest, I never got to the part where they unveiled the true nature of the SAFE test, the SAFE test also has no affect on your gameplay which is odd, it would have made more sense if they called you out for answering in a certain way like they do with every other person who wants to get into their "community"
It was only after watching a video on the covenant by oxhorn doing a deep analysis of the town did I realize they were a bunch of heartless monsters who faked being nice and hospitable, no different from vault-tec. As matter of fact they adopted the SAFE test from them, it was originally called the GOAT test and unlike Fonzy at the front gate questioning you, the GOAT test in fallout 3 has some repercussions for answering in a specific way, not negative repercussions but it still moved the plot forward.
I get that Bethesda didn't want to rise suspicion early on into discovering covenant, but they shouldn't break continuity for a system they coined themselves. That makes no sense
I think what frustrates me the most is covenant is a prestinely kept community and it was just basically used for this quest and most people after that quest will just leave it and forget about it. Yea, there's a workbench but it's not that spacious for a settlement build, there's no reason to go back except if you absolutely need Deezer's lemonade, which in my playthrough he got caught in the crossfire and got destroyed.