Microsoft aren't stupid - the costs they charge for Azure are largely competitive, and the benefits it provides are tangible.
Picking what technology will run your business is something that really needs to be done on a case by case basis, based on your knowledge and your business. Certainly I don't think it's desirable to make a permanent choice when you are still a startup.
Of course you'd use CentOS, unless you had need of the specific features that licensing it gave you.