Well just a little bit ago I helped a legion member take a planet back that was stolen from him, after we dropped the pop and started killing off the guards the only one left was the guy that stole the planet. When his halcyon was tripped he was still on the planet and had to be warped away before the planet could be invaded, I thought this was fixed?

You can still attack someone with a Haly/CAmp while they are guarding a planet FROM THE PLANET SCREEN. However, as soon as you try to use an artifact on the ship, the game forgets that it was while he is guarding and the Truce becomes effective. It's a known issue and one that has been complained about a good bit, but to my knowledge, no changes have been made.