Civil Points now start at level 2 and after that should give points at level 5, 8, 11, 14, 17, 20, etc. I don't think it will retroactively grant you points, but it should hopefully give future points at the right time even on existing saves.

If you're feel like you're missing an extra civil ability point that you should have, then I suggest you use Cheat Commander to add one or two.