As you can see in the link, the function you should use is Player_SetAbilityAvailability.
However, some commander abilities, mostly those that are passive, actually don't do anything and their effects come from somewhere else, i.e. squad weapon upgrades or units that become available in tier buildings. If you want to disable them, you will probably have to do it another way.
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#Steam AliasWL%Streak
- 1.653231.739+13
- 2.838223.790+1
- 3.35057.860+15
- 4.590233.717+6
- 5.278108.720+29
- 6.306114.729+2
- 7.645.928+5
- 8.922406.694+1
- 9.1118621.643-1
- 10.265138.658+2