If you have each client take on the $ burden, then you don't have this problem. You've may have convinced yourself that by absorbing the cost, you are doing your client a great service.

In fact, you are putting more burden on yourself for little value. It takes 15 minutes to walk the client through how to pay for and manage a github organization. I do it with all of my clients. It is an opportunity to teach/coach and give them a sense of ownership which is how it should be.