Other things you can do:
1.) select soldiers with low reactions to carry launchers
2.) keep soldiers clear of the launchers' line of fire
3.) spread soldiers out as much as possible -- this also helps defend against alien grenades and blaster launchers
4.) mod the launchers to have 1 waypoint -- it will prevent them from using reaction fire entirely
My mod, Reaver's Faithful, includes a Heavy soldier class which has reduced reactions.