To me it seems that valuing autonomy is an example of avoid things that may have short term benefits but cause long term problems.

That sounds more like a concern about harm ("long term problems") than about purity, at least if you are trying to describe the thought-process of someone justifying their valuing of autonomy.

If, instead, you are trying to describe the causal origin of the value, then wouldn't Haidt ascribe all of his foundational values to that cause? Doesn't he give ev-psych explanations (with a group-selectionist bent) for the origins of all of his foundational values? If I'm right about that, then he would probably argue that each of his foundational values persisted because, in the long run, it served the reproductive interests of the individual or the group. That is, the value led people to avoid short-term benefits that would cause long-term problems. Otherwise, this value would not have survived in the long run.