Ownership of a site is determined by the account/email that set up the site. It's not just a matter of changing the admin email address on the site later because the site will still be attached to your account and appear in your list of sites. http://en.support.wordpress.com/email-address/
If you are setting this site up for an organization, it would be preferable from the start to open a separate WP.com account using the organization's current email address or set up a new one for that purpose (like webmaster at the organization dot whatever) from the start. This way the organization is the clear owner of the site from Day 1.
If you use your personal account/email to set up their site, you can transfer the ownership of the site to the organization later. However, they will have to create an account on WordPress.com in order for you to do so.
opinion/Assuming that this organization is using email already, setting the admin email account to one on a domain you are setting up for them could potentially cause problems in the future, say for example, should the domain expire. If they don't have an email account, better to use a 3rd party email provider (gmail, outlook, etc.) for this purpose. /opinion
Hope the above is clear. I'm still working on my first cup of morning coffee.