I think most job offerings say CS because they aren't aware of CIS, or will accept CIS as equivalent (unless it's real hardcode low level programming or design required, and you can't list all acronyms). CIS does give you a broader understanding of technology and how it can be leveraged by an organization (but still requires study of OO and algorithms). If you want to move into management it may be your choice. I don't think anyone looks down on it, except for those with insecurities of their own degree (or lack of degree). I am currently finishing my MSc. in CIS. I plan on coupling it with an MBA, eventually. CIS is still definitely academic, otherwise it wouldn't require writing a thesis and would be more of a "learned" degree, like an MBA (which requires no thesis).
Mike