I'm very happy to see you decided to follow through on your plans to work with organic substrates. Of course I am very biased on this topic. :big grin:
I would tell you the benefits of water movement will greater than the loss of CO2. Most of our plants come from water that has movement, there is even thermal current movement in ponds.
One away to use the air stone to lesson the surface agitation, hence lessening the CO2 drive off would be an Air Lift tube. Here's a video that shows the idea on a larger scale in a German(?) pond.
In your tank a simple PVC(Plastic) straight pipe and a elbow(45degree) pipe will create the same effect. By mounting it below the surface you will gets flow with lower surface agitation.
I use PAR38 LED lights too and it is amazing how high they need to be for correct lighting.
Best of Luck with this project, I look forward to seeing your results.