Deadpool was nothing but cool to Cable. Deadpool saved Cable's life-- three times, gave him a power boost, tried to become real friends (for the first time with anyone), helped get him the Dominus Objective (replacing Cable's telepathy), helped get him the Cone of Silence (replacing Cable's telekinesis), helped him become president of Rumekistan (a fictional 3rd world country), all while trying to to play by Cable's goody-goody rules... and in return, Cable turns Deadpool into an unwilling martyr-- twice.
Sure, Deadpool could had sided with Cable in the Civil War. But until that point, Deadpool had been Cable's puppet. Did/does Cable really want to be friends with Deadpool? Or is Deadpool just Cable's pawn?