Specifically, I'd be curious to know if picking one over the other could be problematic later, when applying to a masters program in computer science (the CIS degree is much less theory heavy). I am interested in Standford's MS program, but if I go with the CIS program, I am concerned I will be filtered out in the selection process because I don't hold a brick-and-mortar CS degree with a heavy theoretical focus.
As a mature adult, I have financial obligations that constrain my ability take on studies full time, so I am leaning towards the CIS degree because it is offered through distance education (the CPSC degree is not), and subsequently applying to Stanford's Masters program which is also offered through distance education.
FWIW, I currently work as a developer full-time, and in my younger years I worked on a lot of random jobs, mostly non-applicable to my computer science interests.
The obvious answer here is: if you have very specific programs in mind, and a specific set of constraints that may hinder you, check with the upper-level programs you're interested and find out what their requirements are. If the master's program requires a bachelor's in computer science, then you have your answer. If not, then they may list what degrees they accept as "equivalent" or "sufficient" for their program.
But, in general, when in doubt, ask. That's what graduate officers and admissions staff are there for!