There are no restrictions that can prevent just deleting stock iOS apps. Another way of approaching this would be to set up a policy with a wildcard match (or search for specific stock app(s) you plan on keeping) and an email notification to when stock apps are missing from a device. While it isn't a perfect solution, it does work and we have found it very helpful in situations like these.
As a side note, maybe you would consider creating a profile that puts a restriction profile (i.e. no camera) on the device but also attach a web clip to the app store where the user can re-install the stock app. As soon as the device has the stock app and it checks in woth your server the restrictions and web clip would be removed. This would be a more hands-off approach, but your users will definitely get understand when something they need is hidden for violating a policy your department has set forth!
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