I'm offering two free educational apps with in-app purchases in the App Store. I regularly see educational downloads for both of these apps and I know from feedback from teachers that the apps are used in lessons, but that they apparently cannot do in-app purchases. For that reason I created separate paid versions of these apps without in-app purchases, as you're suggesting. This approach works well for me, and I'm seeing many educational purchases of that paid version of the app.
Unfortunately, there doesn't seem a way to make an app available only for educational institutions, so the paid version will be visible on the App Store, too. So make sure that you're explicitly declaring that new app as an educational version and put an explanation in the App Store description (I'd recommend using a modified app icon, too), otherwise it might confuse other users who don't know which version of the app to use.
