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I personally wouldn't connect a cable directly to a FPGA. Any disturbance on the cable could kill off the FPGA(s).
The direct connection to config_n may/will be vulnerable to disturbances as well.
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Is a Cyclone II more likely to break due to spikes than some kind of dedicated LVDS driverchip?
Meaning: since I'm using the cheapest Cyclone II chips (EP2C5), there is no concern that an expensive chip might break. The only concern is that something breaks. So if the probabilty that something breaks can be significantly reduced by using driverchips between the FPGA and the CAT5, then that is what I'll do.
As for vulnerability of the nCONFIG line, I was meaning to put a pull-up resistor on it to 3.3V at both ends of the line, to make sure that it never spikes down to zero and causes a spurious reconfig.
[Addition]
I already looked it up, and notice that the ESD protection offered by dedicated LVDS buffer chips is a lot higher than that what the FPGA offers (if any). I'll redesign and use LVDS buffers/converters, which kind of automatically solves my problem with the LVDS connected to the FPGA (it won't be, anymore).
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