Secret Clearance - Sponsoring friend

Last December, I visited Vietnam as a tourist and met this guy at a cafe. We chat through Facebook ever since and became close friends. He is currently a student studying IT and holds no government positions. He would like to visit the US as a tourist for approximately 2 weeks some time in the future. He will be living with me and I will be guiding him around the city. We might go to different states during some weekends. I have him listed under foreign contact already, as I feel like this is an obvious example of a close and continuing contact.

Currently, I’m still filling out my eQIP. I don’t plan to make any sponsors though for another 3 years since I need a stable income first.

How likely is it that sponsoring him on a B-Visa would affect my Secret Clearance?

Despite the fact that you have already reported him as a contact, I would stay far away from this and not allow him to stay at your home. This is EXACTLY the way that infiltration/recruitment start.