Pinholes are bad, bro. Once rust hs pinholes it's almost guaranteed to come back again and again.
If you must fill them, you have to use something impervious to water. You might try POR-15 2 part epoxy filler, which cures hard as a rock and waterproof, or even (GASP!) POR-15 "spot putty", which is thick POR-15 in a tube. And definately do something about the back of the panel.