I did some digging, and I think I've found a better solution. By
including some additional .m4 macros in the acinclude directory
(http://www.gnu.org/software/autoconf-archive/ax_check_compiler_flags.html,
http://www.gnu.org/software/autoconf-archive/ax_gcc_archflag.html and
http://www.gnu.org/software/autoconf-archive/ax_gcc_x86_cpuid.html)
then using the patch below (same as previous patch + one line change
to configure.in), SDL will build correctly out of the box.

The arch can then be overridden by --with-gcc-arch=<arch> (most will
probably want to build with i686 there for general distribution) or
--without-gcc-arch, to disable setting the arch all together.

On my Atom netbook, I get -march=PentiumPro by default, which works
great, as does --with-gcc-arch=i686.