Proper way to fix: welding a patch in followed by bodywork and painting. Should be invisible.
Next best: screw and caulk a metal patch over the holes. Obvious but flush with side of van.
Almost as good: metal patch held on by VHB tape or caulk. Again, obvious.
Ghetto: patch taped on with ductape. Won't last long; need to replace frequently. Might not stay watertight.