The commander was feeling a little happy.
He now had the opportunity to nip a threat like Gideon in the bud and didn't need to worry about someone defying him in the future. Moreover, he didn't need to worry about the Patriarch helping Gideon because of the timing was right, then the Patriarch's attention would be needed due to him meeting people he couldn't underestimate.
And he wasn't worried about to repercussions either as the Patriarch would have no proof, and if he was killed for no reason, the pressure on him would rise tremendously, and the so commander doubted that he would throw a fuss and risk something like that happening just because of Gideon.
In his mind, his plan was full proof.