Supposing you want to calm down a raging bull. Is it "manipulation" to remove the red flag from the bull's sight? You're certainly influencing how the bull will behave. But it seems that you're achieving this precisely by removing a source of manipulation (in some sense), and so enhancing the bull's own self-control.
Or, for a human case, consider how we might move the chocolates out of sight, to where they'll be less tempting. Cases like this seem importantly different from, say, brainwashing ourselves (or being 'manipulated' in any problematic sense). What's the relevant difference? Arguably: rationality-enhancing influences (e.g. that counteract prior biases) are innocuous, whereas problematic manipulation consists in influence that detracts from our rationality and self-control. (What about 'rational akrasia'? Perhaps we should understand 'self-control' here as consisting in authentic rather than deliberate-judgment-driven action.)
If this is right, then it seems we shouldn't consider Sunstein and Thaler's "nudges" to be problematically manipulative (or 'Orwellian'), at least if done right. It's surely true that our heuristics and biases can be exploited in manipulative fashion (cf. advertising). But that doesn't mean we have to just ignore our biases. Better to counteract or accommodate them, i.e. set things up so that our everyday heuristics will more often succeed in 'nudging' us in the right direction (by our own lights).
Of course, the "if done right" proviso is a big one. I haven't said anything here to argue against pragmatic libertarian "slippery slope" concerns. I just don't think there's anything inherently problematic with intentionally influencing choices in the modest ways Sunstein and Thaler describe (e.g. changing from opt-in to opt-out organ donation). Like the bull with the red flag, we are being constantly manipulated by our environment into making senseless decisions. We should welcome 'interference' that serves to mitigate the stupidity caused by our natural biases, enabling us to make more rational decisions instead.