Command points should be unlocked automatically via technology stages.

But for a faction that is not focusing on military technology for example, lets say a science focus, they will have a tougher time getting a tech stage up. Meanwhile in the current system they can research technology that is one above their current technology stage due to their science based laws. Wouldn't this basically shift "forced" technology to a "forced" tech stage in the end? What if the unintended effect is that the whole of military tech is even more crucial to compete for victory.

What if we change your suggestion from command points per military tech stage to command points per any tech stage? I can't judge how that would affect things though.