PhD advisor making start up company based on my thesis work. How do I prevent this from delaying my graduation?
How should I approach this? 


Jump at the opportunity! Your professor considers your work a "gold mine" and wants to commercialise. This is an extremely rare opportunity for any student and I recommend that you seriously consider embracing the opportunity. Let me consider some of your ideas and alleviate some of your concerns:


  I prefer to publish it and make most of the data open source.


This is a worthy academic goal, but it mightn't result in your desired outcome. Academics share results for others to build on, yet many results have no impact: If you're hoping your results will have impact, then why not make sure they do yourself? Keep the results private, build a company, make an impact.


  Today, my advisor hired a senior research scientist who intends to learn my work and start a company based on it...The scientist intends on becoming CEO of this company 


Is there any reason to believe that this scientist should be CEO? As opposed to CTO, for instance? Why is the scientist even necessary? Consider taking the CEO role for yourself and maybe consider hiring the scientist. 

Whether your supervisor should be involved is open for debate. They seem well-connected, so they could perhaps be very useful.


  [The senior research scientist] eventually wants equal inventorship


Inventorship (in terms of IP law) cannot be shared: An inventor has to have invented, they cannot come onboard. Perhaps you meant equal ownership? 


  I have argued with him that this work is not ready for a company, and such a start-up would rest on shaky foundations (I have not published or patented, or finished animal studies).


You can start a company, strengthen the foundations, and patent the results. (NB: Your university may actually own the rights to any patents, it depends on your precise scenario. Regardless, you might not need to patent results that would be owned by the university, since patenting later results might suffice.)