Looking around at how other people have solved this problem, one of the better approaches is to offer a single sign-on based licensing solution. (This is an approach Microsoft supports for licensing Office 365, for example.) The idea is that an organization will purchase licenses for use by a team, and the app will offer to let team members sign in with a set of credentials which will be verified by that organization using their single sign-on server. This lets the organization be responsible for purchasing and distributing their team’s licenses — including redistributing licenses when appropriate.
We’ve published a walk-through, with screenshots, showing how it works from a user’s perspective — see How do I install my organization’s OmniGraffle for iOS site license on my iOS device?
If you work at a business or school or other organization, and you might be interested in a site license (for OmniGraffle for iOS or any of OmniFocus, OmniPlan, or OmniOutliner for iOS), please email firstname.lastname@example.org. Feel free to cc Ken at email@example.com.