Upon upgrading to MySQL version 5.1.23 scripts which rely on settings from
the ~/.my.cnf file stopped working.

The problem is that mysys/default.c has the following:

#define MAX_DEFAULT_DIRS 6
const char *default_directories[MAX_DEFAULT_DIRS + 1];

while this currently broken patch to mysys/default.c not only puts
/usr/local/etc/my.cnf into the search path twice, but also pushes
~/.my.cnf beyond the MAX_DEFAULT_DIRS limit:

@@ -1102,6 +1102,8 @@
   bzero((char *) default_directories, sizeof(default_directories));
   ADD_DIRECTORY("/etc/");
   ADD_DIRECTORY("/etc/mysql/");
+  ADD_DIRECTORY("%%PREFIX%%/etc/");
+  ADD_DIRECTORY("%%PREFIX%%/etc/mysql/");
 #ifdef DEFAULT_SYSCONFDIR
   if (DEFAULT_SYSCONFDIR != "")
     ADD_DIRECTORY(DEFAULT_SYSCONFDIR);

The fix is to replace the above patch with the following:

@@ -1105,6 +1105,7 @@
 #ifdef DEFAULT_SYSCONFDIR
   if (DEFAULT_SYSCONFDIR != "")
     ADD_DIRECTORY(DEFAULT_SYSCONFDIR);
+    ADD_DIRECTORY(DEFAULT_SYSCONFDIR "/mysql/");
 #endif
   ADD_COMMON_DIRECTORIES();
   ADD_DIRECTORY("~/");

and get rid of the following from the port's Makefile:
	@${REINPLACE_CMD} -e "s|%%PREFIX%%|${PREFIX}|g" ${WRKSRC}/mysys/default.c

How-To-Repeat: Run mysql --help and look of the line following this:
Default options are read from the following files in the given order:

before the fixed mysql51-server/files/patch-mysys_default.c the output was:
/etc/my.cnf /etc/mysql/my.cnf /usr/local/etc/my.cnf /usr/local/etc/mysql/my.cnf /usr/local/etc/my.cnf

after the fix the output is:
/etc/my.cnf /etc/mysql/my.cnf /usr/local/etc/my.cnf /usr/local/etc/mysql/my.cnf ~/.my.cnf

and of course now ~/.my.cnf settings work once again!