Unfortunately you can't do it right now. The two components of SS distro (CMS and Sapphire) are coupled together and you can't separate them.
However you can build custom apps on Sapphire. What you do is you just ignore the CMS, but leave it sitting in the tree structure so the Sapphire does not complain. It is quite nice framework, I like it better than CakePHP, never used CI nor Symphony so can't compare to that, but I think it's worthy contender with Kohana.
PS. Everyone knows those two should be decoupled, we keep that in mind when we refactor... :)
Sounds like you will be using Sapphire and the CMS together. Build your functionality on top (this is what ss is really good at). Ecommerce i heard is pretty unstable at this point of time, but better check for yourself.