BootChamp no longer works on El Capitan, what's the fastest way to boot into Windows?
You could maybe try to disable System Integrity Protection that came with El Captain. If you want to do so (at your own risk) see Disable System Integrity Protection (rootless).

It's actually what they say on the link you've given :


  I believe this is from changes related to the new “rootless” or System Integrity Protection feature of El Capitan (more info). Whether it’s a bug or a feature is impossible to tell at this point. If it’s a bug, then that means Apple should be fixing it in a future point release, for example 10.11.1. If it’s a feature, they need to update their bless tool and remove the featureset entirely.


The rootless or System Integrity Protection is designed to deny app to edit system related files. The way that BootChamp works it that it uses the command bless to change the current booting disk. This doesn't work anymore with rootless enabled. Other softwares like Refind doesn't work anymore thanks to rootless. System Integrity Protection is there to prevent applications from damaging your computer. It's relatively safe to disable it, but make sure you know what apps are getting executed on your mac.