Anything over-the-counter to add to a water pik after scaling and having deep pockets that can help kill whatever's bad in there?

Iodine tablets: A campers best friend. Add 2 20mg tabs of tetraglycine hydroperiodide per quart of water and wait 30 minutes.

Detergents & H2O2: Since all cells use fat molecules to seperate inside water from outside water, soaps & detergents, which serve to emulsify & wash away fat molecules, tend to destroy all cells, with adequate time and agitation. Additionally, hydrogen peroxide, degrading to water, h20, & releasing o2 is a powerful oxidizing agent which degrades cells, especially bacterial cells which do not function well in air.