At the end I decided to add the -stdlib=libc++ -std=c++11 flags to make when building which means the deployment target doesn't have to be bumped to drastically but just to 10.7 where libc++ was introduced.
This has been committed to the geany-osx project so this one can be closed.
Fixed by referencing here: https://github.com/geany/geany/issues/1618