Definitely not stock. Do you leave your ambient lighting on while driving? If so, since you say its wired into that, you will need to turn off ambient lighting for the time being. I would recommend re-wiring it to a separate switch Or the door unlock circuit rather than leaving it as is. Due to them being aftermarket, I am pretty sure they do not color change. I once saw a similar kit for the emblem from china, but it was pretty expensive and only white/amber.
No matter what you do, the officer was in the right, those are definitely NOT stock, and due to the color not legal. If you dig into the wiring, there MAY be wire that you could connect for a different color (sometimes aftermarket lighting is set up like that). If this is the case you could leave it as is, just swap to the alternate color (white/amber). otherwise, you need to rewire it ASAP.
As for the warning, re-wire it before you get into more trouble. There is a chance if you fix it, that you can go talk to someone at the courthouse and get the warning off of your record as you have fixed the issue.