I'm not an expert at all, but I think that Clover has nothing to do with the EFI eeprom chip on the logic board. It is just installed on the EFI partition of your hard drive, so probably the problem is more related to the EFI partition.
One time when I was working to install on a Lenovo laptop a hackintosh, I installed clover by error on my iMac's fusion drive, so I had to remove the drives from it and install os x on them again from another Mac. Then it booted again.
In fact there is an USB image that allows you to download El Capitan from the App Store on a Mac Pro 1.1 or 2.1 that it's an Clover USB with no injections, it only changes the Smbios for one of the Mac Pro 3.1, so you can download El Capitan on those Macs.
I guess that the only way that clover can brake your system is if any kind of SSDT, injection or something similar makes a hardware issue by overheating something. But I have no idea about this.