I can't stand this secular inquisition bullshit of cherry picking any sign of possible 'out there'-ness and using it to completely trash peoples' entire bodies of thought and work. It's anti-scientific. Please point out a problem with Brandenburg's actual published work, or go away. Even if he does hold non-traditional or strange religious beliefs, it's not relevant. Roman Catholicism is no more rational than Eastern mystic cults, so do we throw out all scientific papers by Roman Catholics?
I'm not much of a fan of PZ Myers either. I read him a bit back during the mid-2000s 'intelligent design' creationist PR offensive, but stopped reading him as he got more and more shrill and irritating. IMHO Myers is as much a shrill fundamentalist as the religious bozos he constantly wars with.
One interesting thing Brandenburg did say was that when he came to believe himself that Mars had been nuked, possibly in act of "biosphere genocide," the realization that this might have actually happened plunged him into a bit of a metaphysical crisis. He immediately thought of the Fermi Paradox, and that maybe the reason we're not hearing/seeing anything is because there are big nasty genocidal intelligences out there that 'cull' anything interesting from the universe. He said he actually got very depressed, and got deeper into religious/mystical stuff as part of this.
That doesn't sound crazy to me, just human. Around here we've seen some IMHO irrational fears of super-human dangerous AIs circulating recently, and it seems to have led to a similar amount of metaphysical anxiety among some very brilliant and notable people in the CS field.
I'm very skeptical of Brandenburg's thesis here, but I have to admit that the evidence he puts forward is very interesting. It either points to what he says -- some kind of incredibly ancient use of a nuclear device -- or an as yet undiscovered natural phenomenon that can yield a similar signature.
One possibility (other than 'reaper' aliens) I can think of would be a natural nuclear reactor that actually went fully supercritical and detonated. Another would be a hypervelocity object, possibly traveling at some significant fraction of the speed of light, that impacted Mars and went thermonuclear in the atmosphere on kinetic energy alone. Maybe an asteroid or comet that got flung by a high-gravity body (black hole? neutron star?) or supernova debris could do that?