FreeCAD does not start anymore due to missing libboost_program_options

Are you sure that you have libboost_program_options.so.1.49.0 in /usr/lib/ then?
13.1 comes with boost 1.54 only.

Also do you have a 32bit or 64bit system, is the FreeCAD you installed the 32bit or 64bit version?
The 64bit version would expect the libraries in /usr/lib64/ instead.

But if FreeCAD requires boost 1.49, the package is definitely not intended for 13.1.

Btw, the latest version (0.13.99+git20140610.1336) is available on Packman. Install that and it should work, it is available as 32bit and 64bit package.