How about this (or some such) change in _AC_INIT_DEFAULTS? I surmise it isn't an issue with current systems. At least the hostname on mine (CentOS) returns zero. And anything using GNU hostname is hopefully ok.
BTW, the only reason I notice this is because I routinely grep sources of new packages submitted to GNU for "Linux", and this always comes up :). Thanks, k --- /usr/local/gnu/src/autoconf-2.63/lib/autoconf/ORIG/general.m4 2008-08-22 14:05:31.000000000 +0200 +++ /usr/local/gnu/src/autoconf-2.63/lib/autoconf/general.m4 2010-06-13 01:47:54.000000000 +0200 @@ -384,3 +384,3 @@ # Name of the host. -# hostname on some systems (SVR3.2, Linux) returns a bogus exit status, +# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status, # so uname gets run too. Diff finished at Sun Jun 13 01:47:56