How, exactly, does the NCR seizing Helios One differ significantly from the Enclave taking control of the purifier in Fo3? Yet the Enclave was painted as pure evil, for the exact same action, because of the "OMG they killed mah daddeh!" audience manipulation plot point. Which, by the way, they didn't even do. James commit suicide to keep them from wresting the project from him.
There is very little similarity, really.
The Brotherhood and the NCR were waging a war for dominance.....and Helios 1 was a legitimate military target, both because of what it was and the fact that the Elder of the local BoS chapter foolishly chose to make his final stand there. If you are at war with your enemy, and he chooses to mass his main strength in a indefensible position...the logical response is to exploit their mistake, which the NCR did and broke the back of the BoS in the area. The Courier learns that the NCR would have paid dearly if the BoS had been left to unlock the secrets of Helios and get the facility on line, as they would have used ARCHIMEDES on the NCR forces without hesitation.
The Enclave, on the other hand, did swoop in and steal PP from it's rightful owners, with the intent of perverting thier work into either a instrument of genocide (Eden) or the foundation upon which a fascist Dictatorship would be erected (Autumn)....just because they could. After they respond to even passive resistance by summarily murdering a noncombatant who presented no threat at all, James floods the purifier with radiation, resulting in his own death, so the LW and the rest of the PP staff could escape before they ended up like poor Janet. Autumn proves him right if the LW cooperates at Raven Rock by killing him/her once the purifier is on line.