The Brotherhood in new vegas are cruel. They put a explosive collar on you just for being in their bunker, they tried to kill you, and they are aggressive. How come killing them nets you evil karma per kill? This mod changes that.
The brotherhood aren't cruel persay, they are just very secretive, if the NCR or outside powers knew they were still alive, as Evident by the mainquests for each major faction, they would send troops to wipe them out.
Putting a collar on you for discovering them is MUCH more merciful than just outright killing you like they could have, and to top it off, the leader of the brotherhood doesn't care if you spare the NCR ranger by destroying his radio, further proving that the brotherhood arent as cruel as you say, the Brotherhood were forced into a war with the NCR over hoover dam, the brotherhood owned it first but the NCR wanted it for the power, so naturally they dislike eachother and with how big the NCR is, the brotherhood obv are going to be scared and this further justifies their actions.