Here is a few quick dumps that lead fairly well into the question:
1 - Showing our PHPGD is compiled with freetype support
[root@... php-5.3.8]# php -i | grep Free
FreeType Support => enabled
FreeType Linkage => with freetype
FreeType Version => 2.3.11
2 - HTTPD child pmap showing the freetype libraries are loading (as expected)
[root@... php-5.3.8]# pmap 31638 | grep free
00007f1edd426000 604K r-x-- /usr/lib64/libfreetype.so.6.3.22
00007f1edd4bd000 2044K ----- /usr/lib64/libfreetype.so.6.3.22
00007f1edd6bc000 24K rw--- /usr/lib64/libfreetype.so.6.3.22
3 - Showing that ./configure (5.3.8 source) has no way to disable freetype support
[root@... php-5.3.8]# ./configure --help | grep free
--with-freetype-dir[=DIR] GD: Set the path to FreeType 2 install prefix
So, I think the above sums the question up fairly well:
How do I go about disabling FreeType support?
I just used FreeType as an example, but there are countless other examples where ./configure has no way of disabling 'features' of php (or its extensions) that we never use (such as FreeType support).