In 99% of cases going with an ex-enterprise sysadmin for your CTO for a early-medium stage startup is a horrible idea. Sysadmin needs are significantly smaller than programming/engineering needs until you get to a really big scale. So, while either is probably OK if they are overall smart and good at tech management, my advice is go for someone with experience managing programmers vs. someone with experience managing sys admins if you have to choose. Ideally you get someone who has been CTO at a startup before and has experience bridging this particular gap.

The third aspect of this is management. Someone who has been in management for 10 years is not going to be a spectacular programmer or sysadmin because they simply wont be up to date, but they've got a solid tech background and great managerial skills. These tend to be better later hires, but could be right as well depending on your situation.