Protecting a laptop from USB connected devices
The real problem is not the unprotected USB port, the real problem is that your device puts you and your devices at risk of being connected to higher-voltage, relatively high-current sources.

You can solve transient overvoltage with clamping diodes, but these won't help if you power supply is strong enough – they will just fail, and then you're in the same situation as before, only milliseconds and the smell of burnt semiconductors farther.

Your problem is a bad one, for a lot of reasons, and your laptops are the least of that: 

USB is meant to be handled manually (that's redundant wording), so if this fault kills your laptop, I don't have the strongest confidence that it's inherently save for human interaction.

There is, for good reason, design criteria for circuitry that involves switching higher voltages with lower voltages. 

Generally: you need galvanic isolation between whatever any human (even a service technician) could touch during operation and the dangerous voltages.

Hence: strictly separate your USB controller and the things it switches. It's common practice to drive inductive or high-voltage loads using optocouplers, whose secondary side is driven by a separate power supply. 

The board layout must make the high-voltage regions separate from the 5V/MCU environment. Only optocouplers, transformer cores, and relays can be allowed to cross that boundary. No compromises.

A typical problem is that your device's power supply ground has a completely different potential than the USB ground – though that should not be an issue for a laptop, which itself should be galvanically separate from anything else, there's a lot of cases where you run into trouble with that (e.g. laptop ground ends up on ethernet ground, audio ground, RS-232 ground...). The strict separation (isolation) between controller and controlled makes that an inherent non-issue.