This article very distinctly describes passivation vs pickling.
Clearly, passivation works best on clean "bare" metal:
And that's the part I need the most help with. The article above talks about using nitric-acid. So back to the beginning...
1. Reduce as much of the need to clean up thermal oxides by not producing them to begin with. Better solder technique, (different flux?)
2. Find the least toxic environmentally safe chemical way to remove any oxides produced that can't easily be removed mechanically.