One of the most insidious things about the India nuclear deal (which The New Republic has opposed for these reasons) is that its value derives from us breaking the principles of the nonproliferation regime.
That's because so much of the deal's value is psychological. Its architects have sold it as a paradigm-shifting gateway to a new strategic relationship, in which India will finally join the family of Westernized, Democratic great powers and ally with the United States.
But how, one might ask, is a simple technology-sharing deal supposed to accomplish all this? Unless there's a fundamental change in their own interests, India's strategic goals will remain largely the same: They will not start containing China simply because they're using GE reactor parts; nor will they suddenly halt cooperation with Iran. And the development benefits of nuclear power are small, hype notwithstanding--they can't possibly reorient India on their own.
No, the only paradigm-shifting aspect of the deal is related to India's belief that the Nonproliferation Treaty is a form of "nuclear apartheid," which has kept India a second-class citizen in a world of nuclear great powers. In that view, the United States is breaking the chains of bondage that have held India down for decades. As a Council on Foreign Relations primer puts it, the deal would "gut" the NPT--dismantling a system that India finds fundamentally unfair and granting it recognition it has always felt it deserves.
Any U.S.-India "alliance" would be built on this interaction--and, as such, undoing America's commitment to the nonproliferation regime is the essence of the India deal, rather than an incidental result of it.
Update: See more bad things about the India deal here.