Should I leave my "first" job for a PhD student position?
You did not mention how do you feel in your current job. Do you feel that you are learning a lot, are you enjoying it? If the answer to this is yes, and seeing as it is a private research institute, then maybe consider staying there. There has been a lot of articles around about how you do not need to have a PhD to be successful and satisfied in your career. 

Another point to consider is, why did you get this offer despite your GPA being so low? And maybe your GPA being low is an indication to you being able to grow more in a job at a research institute, as the environment, different from academics, may suit you better and you would end up learning more here. Or maybe your GPA is low for other reasons, and it does not always reflect how you strive in a PhD program anyway.