There were exFAT (aka FAT64 aka fatx) patches floating around for Linux before. In the worst case it will end up like (the unofficial) DVD support in Linux where it's available legally in some countries but its distribution is restricted in others. Eventually Linux also got a closed source, commercial DVD player, but I doubt anyone pays for that except OEMs. If the licensing isn't worked out, things may end up the same way this time.

All that being said, MS is against software patents, so suing some open source developers over implementing this or distributing it would not really mesh well with their lobbying activities. Also, recent court cases (in the US at least) have challenged the idea that things like business plans and software are even patentable.

Hopefully this will all have worked out in favor of Linux/Mac OS by the time these things are even on the market.