The player destruction logic entity was updated a while ago to include the input:
SetPointsOnPlayerDeath <integer> Set number of points per flag dropped upon player death.
which you can set via a logic_auto's OnMapSpawn to 0.
Meanwhile flags were also updated then to include the keyvalue:
Point Value PointValue <integer> Player Destruction or Robot Destruction mode: Point value of this flag pickup
which you can put on a flag as 1 (or more) that is set up on a
point_template - of which you can then send an input of ForceSpawn to spawn the flags in the map, multiple times over from the same template if need be.
I'm not sure specifically how
@Yrr made af_rapture but I suspect it was about the same.