We dont even know if they were really his own people, that is pure speculation. All we know is that Fury had Shield people working on this off the books, that does not mean that those guards were also SHIELD. Even so Coulson made the right call in that episode and people need to get over it. He repeatedly pleaded with them, and they showed no concern at all for the very fact that it was obviously SHIELD coming in, or for the well being of the injured.
Could they have used the stun guns? Maybe, maybe not (in taking a military facility of unknown capabilities, you would always want a conventional fire arm for the penetrating ability and stopping power).
But if those guards were really SHIELD, they were also complete morons for not at least attempting to ascertain the validity of the situation. Had the situation been reversed, Coulson and his team would have tried to understand the situation, not just shoot to kill. o not forget that it was Ward and Garette that did the killing, Coulson wanted to give them medical attention after they were down, there is no redemption arc necessary for him, he did nothing wrong and tried his best to defuse the situation given the circumstances.
Attack sloppy writing if you want (stun guns not being brought) but Coulson did nothing wrong and intended to try and save the guards lives.
Keep in mind, re lethal force, these guards were of unknown training (presumably quite good) and were shooting at the team with fully automatic assault rifles.