Will an industry funded PhD hurt one's research career?
I see no inherent problem with industry funding for Ph.D., and in many cases it can be a benefit.  Certainly in computer science there is a broad spectrum of options for different types of research career (government, large industry, startups, etc.), and it's not unusual for people to move between them multiple times over the course of a career. As long as you are publishing well and frequently, you'll have lots of options.