I'm pretty sure that macdeployqt isn't working correctly for code that's protected. It appears that the @rpath items in the executable are not being allowed for this code. You can use @loader_path instead. But fixing that would require not only fixing the paths in the executable itself, but also in the Framework libraries.
I'll file a bug report for this, though I'm really not familiar with OSX it appears this is the way things are supposed to work.
BTW I'm STILL seeing the crash in the plugin--unfortunately I'm not getting any useful crash report. It looks like what happened earlier; the code is failing in createPlatformIntegration. I see these messages in the Console log:

8/18/16 3:14:17.054 PM com.apple.xpc.launchd[1]: (com.apple.WebKit.Plugin.64.E77BAC61-F958-4FF7-9D28-01F88EAF0E5C[2660]) Service exited due to signal: Abort trap: 6 8/18/16 3:14:18.154 PM com.apple.WebKit.Plugin.64[2661]: Failed to connect (colorGridView) outlet from (NSApplication) to (NSColorPickerGridView): missing setter or instance variable 8/18/16 3:14:18.154 PM com.apple.WebKit.Plugin.64[2661]: Failed to connect (view) outlet from (NSApplication) to (NSColorPickerGridView): missing setter or instance variable 8/18/16 3:14:18.000 PM kernel[0]: Process[2661] crashed: com.apple.WebKit. Too many corpses being created.