So what is a "special system operation modes"? The next thing to do is to search the entire Reference Manual for that phrase ... and that's the only mention.
So search for "special system" and match on "special system test modes" in the same chapter, but nowhere else.
So I'm now guessing that that the ability to override the "write once" characteristic might be shared by other "write once" bits, like the ones in SOPT1. No, they seem to be only write-once with no documented override.
The problem here is that these chips are assembled from "modules", and those modules come with documentation chapters, which are put together to make the Reference Manual. Phrases and keywords in one chapter may match similar keywords in other chapters FOR OTHER CHIPS, and even other FAMILIES of chips (ARM, PPC, HCS12), but the particular set of chapters for your chip may not match up as well as other Reference Manuals. So it is worth performing "archaeology" on different manuals to see if you can see where that phrase may have made more sense. The CAN Silicon Module has a "pin" on it which controls the CANE bit, and indicates the CPU is in a "special mode".
Surprisingly, searching Freescale's site for "CANE that is write once in normal and anytime in special system operation modes" only gets a match in that manual.
Searching for "anytime in special system operation modes" gets 10 matches. One match is in your manual, but the other 9 are in "9S12" manuals, which shows where this CAN module was previously used. So it can be reset in a 9S12 "special system mode", and the chapter only makes sense when read in an MC9S12 Reference Manual.
Sure enough, in the MC9S12Q128 Manual it says the CPU can be in one of 8 modes controlled by MODA, MODB and MODC pins, and some of those modes are considered to be "4.4.3.2 Special Operating Modes".
The MCF51 CPU has Debug, Secure, Run, Wait and 4 Stop modes. If forced to guess I'd say the "Debug" is the only "Special Mode" here. and that the MCF "Debug Mode" wire is connected to the CAN module's "Special Mode" input.
Which doesn't solve your problem at all. There's no way to get this pin to be GPIO. Your only option to "blink a LED" would be to transmit CAN data on that pin, but note you can't usually or easily stop it transmitting if it can't finish transmitting.
Tom