Is is possible to deactivate the Lightning port?
No, any version of iOS doesn't allow the deactivation of the Lightning / 30-pin port.

Plugging an iOS device into a new computer will prompt a message on the device whether or not to "trust" that computer or not. "Trusting" a computer allows normal access, otherwise the device would only charge and disallow any data transfer... although it seems in your environment that would be of little benefit.