How do I configure it myself? Do you have a reference?

Modify the Debian packaging files to provide the correct compilation options - sorry I'm not experienced with this as I've only made RPMs before =- but it should be pretty easy to figure out.

I think that Ubuntu enables hinting on default. According to FreeType's docs/TRUETYPE the TT_CONFIG_OPTION_BYTECODE_INTERPRETER macro should be defined, should you want to enable patent encumbered parts.

On a karmic box:

  $ apt-get source libfreetype6
  $ grep -h TT_CONFIG_OPTION_BYTECODE freetype-2.3.9/debian/patches-freetype/*
  -/* #define TT_CONFIG_OPTION_BYTECODE_INTERPRETER */
  +#define TT_CONFIG_OPTION_BYTECODE_INTERPRETER