Answer by Ricipedian
It sounds like there were a combination of reasons. As near as I can figure :
1. The Obama Administration made the GM restructuring look like a sale, in order to make the rules more favorable. This kind of shenanigans was supposedly outlawed in 1978.
2. Some of the bond holders were financial institutions that were benefiting from TARP, so they weren't in a position to risk the wrath of their governmental benefactors by objecting.
At first, the fact that the companies' creditors (and especially Chrysler's creditors, who were so badly mistreated) put up with such terms and waived their property rights seems astonishing. But it becomes less so — and sheds more light on how this entire process imperils the rule of law — when one considers the enormous leverage the federal government had over most of these creditors. Many of Chrysler's secured-bond holders were large financial institutions — several of which had previously been saved from failure by TARP. Though there is no explicit evidence that support from TARP funds bought these bond holders' acquiescence in the Chrysler case, their silence in the face of a massive financial haircut is otherwise very difficult to explain.
Indeed, those secured-bond holders who were not supported by TARP did not go nearly as quietly. 
3. It became a fait accompli. GM could argue that the Obama Administration wouldn't do the deal unless it rewarded its political allies at the UAW, making liquidation the only alternative.
- Todd Zywicki, "The Auto Bailout and the Rule of Law," National Affairs, Spring 2011. http://www.nationalaffairs.com/publications/detail/the-auto-bailout-and-the-rule-of-law