Try running
git config core.fileMode false
This is a git thing, nothing to do with Java or SmartGit in particular, just that we don't properly support Unix permissions.
Be aware that if you create patches for upstream, people may get pissed off when you change/remove the permissions from shell scripts such as configure so double check.
You could also use chmod.exe to change the permissions. Something like (untested, just copied from the internet)
find . -type d -exec chmod a+rwx {} \; # Make folders traversable and read/write
find . -type f -exec chmod a+rw {} \; # Make files read/write
Make sure you use the correct find, namely the one in @UNIXROOT/usr/bin