In Xcode 7 Apple has switched from GCC assembler to LLVM assembler. Even when using GCC to compile, it uses the system assembler. This (or maybe something else changed as well) led to problems compiling DFHack and plugins. When compiling with GCC 4.5, some of the resulting binaries crash, including the protobuf compiler that's build during DFHack build process. When compiling with later GCC versions, the new assembler can't compile one of the produced by GCC files.
Fortunately, you can have several Xcode versions installed, so you can install Xcode 6 to /Applications/Xcode_6.app (don't use path with spaces, as cmake will fail), and switch to it when needed with
sudo xcode-select -s /Applications/Xcode_6.app
Also the following symlink is required due to some library changes:
cd /usr/local/lib
sudo ln -s ../../lib/libSystem.B.dylib libgcc_s.10.5.dylib
And this is required because the old GCC doesn't know about newer systems (I've tried 10.5 but cmake failed, I think supporting 10.6 is enough nowadays):
export MACOSX_DEPLOYMENT_TARGET=10.6
With this, I was able to build working DFHack and my plugins on 10.11 with GCC 4.5 and Xcode 7 installed (besides Xcode 6). As I understand, xcode-select affects only console tools, so you can continue to run and use Xcode 7 for other development.