There is no way to just log out of your email account in the Mail app on the iPad. All you can do is delete the account, then add it again when needed. Not a very good solution.
If you need secure email then I recommend you use your provider's webmail client through Safari (and remember to log out), or a third party email client like ibisMail.
Hold in mind that in order to use mail from within other apps you will need a working email account set up on the iPad; but it does not need to be your primary account, as long as you don't mind sending those emails from that second email address.