For one thing, not all of the US's potential adversaries are radical Islamists. In future conventional wars, we will need the moral authority to demand that our prisoners be treated in accordance with international laws and treaty obligations. Debacles like Abu Ghraib -- to say nothing of the Iraq war in general -- rob us of that moral authority, in much the same way that the Roman Catholic Church loses some of its moral authority every time another child sex abuse case comes to light. To occupy the high ground, you must first take it.

The OP made mention of how Manning's leak directly led to intelligence sources imprisonment and death.

No, orchestrating a bogus public health campaign led to Afridi's imprisonment. As far as I'm concerned, Afridi can take his place next to Mengele in medical infamy.

Manning did an unalloyed good thing in bringing the CIA's tactic to light [1]. I want foreign operatives to tell the Agency to fuck off when they come up with ideas like, "Hey, let's start a vaccination program so we can subvert the local populace and find our bad guy."

You seem to think that the ends justify the means. That's great, as long as you have perfect knowledge of future consequences. In that sense, both the US government and Bradley Manning made the same logical error. The difference is, his actions had some positive consequences as well as negative ones.

[1]: If, in fact, he did. There seems to be some disagreement with briandear's (lack of a) citation on this.