I would taboo the word "autonomy" in this context, or at least give a clear definition, because there are at least 2 different things that it could refer to.

In Haidt's six foundations theory, the closest thing to "autonomy" as it is being used in this discussion is probably the liberty/oppression foundation (the 6th foundation to be added):

Liberty/oppression: This foundation is about the feelings of reactance and resentment people feel toward those who dominate them and restrict their liberty. Its intuitions are often in tension with those of the authority foundation. The hatred of bullies and dominators motivates people to come together, in solidarity, to oppose or take down the oppressor.

The liberty/oppression foundation is somewhat underdeveloped in Haidt's book, and discussed separately from the other foundations in a way that's organized a bit strangely, probably because the book was already in progress when he decided to count liberty/oppression as a sixth foundation. Haidt does not seem to have any published papers yet on the liberty/oppression foundation, but he does have one under review which focuses on libertarians.

In Richard Shweder's three-area theory, which was the original basis for Haidt's theory, "autonomy" has a different meaning. It is one of the three ethics - "autonomy" is the blanket label given to the individualistic/liberal approach to morality which involves harm, rights, and justice. The ethic of autonomy is contrasted with the ethic of community (ingroup and hierarchy) and the ethic of divinity (purity and sacredness). In one of Haidt's earlier papers, which used Shweder's system, experimental participants were given this definition of autonomy:

The ethics of Autonomy Individual freedom/rights violations. In these cases an action is wrong because it directly hurts another person, or infringes upon his/her rights or freedoms as an individual. To decide if an action is wrong, you think about things like harm, rights, justice, freedom, fairness, individualism, and the importance of individual choice and liberty.

If you look at that definition and think "but that's all of morality, mushed together in one big category" then congratulations, you're WEIRD. In Shweder's approach, being obsessed with autonomy is precisely what is distinctive about liberals. The utilitarian, who applies cost-benefit analysis to everything and is willing to make any tradeoff, is just one member of the autonomy-obsessed family of moral perspectives. People who rigidly apply concepts of rights, liberty, or justice are part of that same family. The grand Kant-Bentham debate is just a factional squabble which is happening in one corner of the moral triangle.

Haidt's six-foundation approach can be considered a refinement of this view, which keeps Divinity, splits Community in two (ingroup & hierarchy), and divides Autonomy in three (harm, fairness, and liberty). Although there are some complications (fairness is somewhat Community-tinged, and liberty might be too).