I definitely wouldn't recommend changing every include.
Can you configure freetype to go straight into /usr/local/lib and /usr/local/include instead, with no freetype/? That would be how I would attack it. Most libraries are going to have a way to configure them to go where you want them to go. GNU Stow can be very useful here to keep things organized.
What distro are you using that doesn't have freetype available? That seems strange.
Who was it on Twitter, do you remember? You might be onto something.