When the agent avatars where first presented to the player community some did like it and change their avatars and some didn't. There was and still is a problem for those who did try the avatars but later wanted to revert back to the original logo. They couldn't revert back to the original clear faction logo.
Does anyone know of a way to clear the background to the original transparent faction logo on the avatar?
There is currently no way to turn back to a transparent background. Maybe this will be patched in the future?
I was bugged by the problem when I reached level 2. Later I solved the problem by doing a faction change(resistance to resistance). I didn't do it just for this particular problem though. The whole process took me less than 24 hours despite Niantic saying it might take 7+ weeks to review and process. Once the faction change process is completed, you will lose all your live resonators and mods, all you APs and all items excepts powerups and keys in your key lockers. You avatar background will also be returned to the original faction logo. Just remember not to change it again when you reach level 2.
You probably don't want a faction change but technically it solves the problem.
