Well, in all honesty, she was in charge, and she may have been incredibly decieved herself by who was on this case, but alarms should have went off when some of the suspended Ruby Ridge officials were assigned to this. One was later put in prison for destroying evidence in that case.
As far as his beliefs go, he thought he was going to die in a war with 'Babylonians riding chariots', whcih he interpreted to mean he was going to die by FBI Agents and tanks. Mercy killing was ok to them during this and would be honorable. So Yes, I think they killed themselves, but I can't even be sure of my assumption because of the massive fuck-up that happened.