Thing is, virtual memory ought not to destroy your SMC, at least if its possible to get access to the MMU and do it GPAdvance style. The reason being that you're actually talking about a ROM - so a static bit of memory that is unchanging. In other words, virtual memory containing a rom need only be the position of the rom on the SD card with some form of mapping such that when the emulator asks for a bit of the game that currently is not loaded, the right bit gets loaded and subsequently accessed from the right place in RAM.
Slow, but it doesn't kill your card.
What *would* kill your card would be if the original system had, say, 128MB of ram, and you were trying to use a portion of the SD card to make up for that. As far as I'm aware, this is not the case with the Neo Geo, however, MVS or no. Indeed, according to the specs I've found, the system only actually had 64k of internal ram, another 64k of video and 2kb for the Z80 chip - hardly of card-shattering quantities.
That is not to say virtual memory is entirely possible currently... iirc, at one point it was thought that Linux would make it hard for coders to use the MMU correctly, thus removing it as a possibility whilst the original loader was in use, but I don't know if this is still thought to be the case.