I don't think they should be awarded from experience directly, simply come in a slow drip every few months automatically. Coming faster when you have none and slower when you have a stockpile. They're supposed to represent moments of exceptional ingenuity, cleverness, skill, luck, etc. It makes sense from a narrative perspective for our intrepid hero to do pull off such feats sporadically, but as is often the case I find myself with 15 or more and my character waltzes through my colony knowing exactly how to optimize every industry, graces my chief engineer with brilliant plans on how to push our best ships to their absolute limit and perform beyond our wildest expectations, and then gets on comms to charm politicians. What a day!
If prefer they come in over time to encourage using them, and to prevent grinding later in the game. Colony SP improvements could simply allow you to put one point in at a time until you get the required amount for the improvement.