Send me a PM here at MT. I will help you. It might take a few days. I will need some more details.
Based upon what you have told me, you want only data files\document files to come off the USB onto the system. If you control what the USB can and cannot do when connected to the workstation, then most of your problem is solved.
You can use freeware USBFlashDrive Control from Binisoft.org. Set it to Read-Only mode on the workstations. Users can copy documents\database files and paste them to the workstation. They cannot open anything from the USB itself.
The problem is that you cannot password protect the settings - so you will have to teach users not to mess with the settings. If you do not explain anything else, they probably will not figure out that you have to disconnect and reconnect it after making a policy change. So they probably will not figure out how to change the settings.
Also, they cannot copy the entire drive contents and paste to the workstation - they must copy-paste only the specific files that they need. So there is some reliance on the workstation user always doing the right thing.
Also, there is freeware SRP that you can install on workstation windows. Set up policies to prevent launches on USB and desktop other than documents\database files. This is added protection when the user gets lazy and just copies the entire USB contents to the desktop or other user space location.
That way you have a primary, secondary and tertiary protection in-place = Binisoft USBFlashDrive Control, SRP and Quickheal.
I assume you will have workstations set to use Standard User Account with enforced, password protected UAC.
As for server protection I will need more details and have to think on it. A lot depends upon what kind of scripts the softs employ - .ps1, .js, .bat, .wsf, etc, etc.