For transportation, we could just have the civilians walk.
In case this reply wasn't facetious, I absolutely do not recommend having the civilians walk. Civvies are slow, vulnerable, and prone to do all sorts of stupid things while we try to save them from (admittedly, afflicted by us) fiery death. We also do not want them to know the route back to their homes so they have no choice but to stay where we put them rather than risking some of the bolder and dumber ones from trying to escape back to their ancestral home.
Furthermore, by knocking out all of the civilians as we apprehend them we have better odds of ensuring no disguised Rock and/or Cloud ninja surprise and ambush us, learn where we take the civilians and then exfiltrate, or simply kill all of the civilians rather than let us have them as we transport the civilians.
Even if this solution saves more lives than letting scorch squads continue as normal, it still leaves a bad taste in my mouth since relocation on this magnitude eerily reminds me of the
Trail of Tears. Treating even imaginary people essentially as cattle to be used as productively as possible without respecting their agency as people feels too close to accepting MfD!Sasuke's arguments about civilian rights to my sensibilities.
I guess this is what happens when super powers are directly connected to genetics and events progress realistically. Unalienable rights become almost untenable when the dominant minority have otherworldly means of enforcing and ensuring their rulership. We still have to ensure there is a world for a just society to exist in so we have to save the civilians as best we can but we're certainly starting from the bottom in terms of social progress when it comes to universal civilian rights.
On a meta note it's interesting to see MfD reflect
Maslow's Hierarchy of Needs in how we (or at least, I) choose which problems have to be solved first.