You CAN use Filena’s Combo Throw and Combo Melee Attacks, Turrets and your own Melee to kill enemies.
I think during the flashback missions, you can use any weapon.
btw. can you do this out of order? like finish a few levels, skip a few, play through the last ones and finish with the ones you skipped, adding up to a full playthrough? I am playing through the game on hard right now and after finishing mission 6, is started mission 7 on easy, played for a bit und then started mission 7 again on hard to continue.