If you upgrade to macOS High Sierra, third-party kernel extensions you had previously installed will be fine.
But if you didn't already have those installed and want to install them, you'll get an error like this:
There isn't a way to script that away—the user must actually click Allow.
Probably the most practical way to deal with this for large deployments is to make sure your client machines are all enrolled in an MDM.
The MDM doesn't have to do anything to the client or push any special profiles. The clients just have to be enrolled. If they're enrolled, there won't be a prompt to allow installation of third-party kexts.