I believe it has to do with the principle of "credit where credit is due". Intel designed the x86 instruction set, so i386 bares the 'i' from Intel. With AMD having designed the 64-bit extension to this instructionset and having it called AMD64; it's only consistent to call platforms on this architecture with that name.
The alternative would be to not give any credit and use neutral x86-64 identifiers, but then i386 should be renamed to x86 or x86-32 as well. Though perhaps confusing to some, I do believe the amd64/i386 names that FreeBSD use are preferable to the alternative just given.