macdeployqt doesn't work for protected executables

I'm using Qt 5.5.1 as part of an Internet Plug-in on OSX 10.11.5. When System Integrity Protection is turned on, the plug-in fails to execute. The Console log shows that the plug-in is not getting loaded, with errors showing that the Framework components inserted by macdeployqt are not being found.
I traced this to the use of @rpath in the executable. It appears that for protected executables, this isn't allowed (I'm not very familiar with OSX, so I'm kind of guessing here). There are @rpath references in the executable and in the Qt Framework libraries. The binaries pointed to by these references don't seem to load.
When I used install_name_tool to use @loader_path instead the load problem resolved. This requires applying install_name_tool to the executable as well as to the Framework libraries.