Well, saying "he may be bad but THOSE guys are worse" is hardly a sterling defence.
His wife was an esper. If he had told her the truth she would have known it, just like she knew he was holding something back. And he already knew the Shedai were a threat, otherwise why try to warn her off, however obliquely, in the first place?
The death of an innocent, as happened to Zeke, is a tragedy. Once done, there's nothing that can be done to correct it (time travel notwithstanding).
Allowing someone to get away with allowing the deaths of hundreds of civilians is a travesty. Unlike the situation with Fischer, Reyes is still around to face up for his crime. Letting him live happily ever after is rewarding criminal behavior.