It's something we see after Deadshot's son was killed because of his mother's actions.
Right after that happened, Rick Flag went AWOL to kill a Senator to protect the squad. The team was dispatched to stop him, to 'stop Flag from shooting Senator Cray at all costs'. Deadshot, pretty around the bend at the time, found Flag and Cray first.
Instead of stopping Flag, however, Deadshot shot Cray and bragged to Flag (he called him Eddie at the time, the name of his older brother) that he did it to the letter, just like Ma wanted (after all, he stopped Flag from killing the Senator).
In Deadshot's mind, he was reenacting the family tragedy that created his death wish. Originally, his mother wanted him to kill his father, but Eddie stepped in for Floyd. Floyd tried to stop it by shooting the gun from Eddie's hand, but the branch he was on broke so that he shot his brother.
So yeah, Waller=his mom, in Deadshot's mind. Pleasant thought, no?