Well to be fair this was always the case. But you’re also making a few wrong assumptions here:
1st at any given time something can change that will make un-official tools/script stop working, this IS the risk of using them.
2nd the script is on github anyone can help and submit PRs to fix it (seems like some folks are already doing it)
3rd You can still replace the binaries, no one said you can’t… you own you’re on system if yo want to do it that way its up to you… (I did say in a previous post that this wasn’t the official way to update, perhaps you took it as you can no longer do that, but that’s not true)
I would also like to note that this changes are in the works for some time now, and make things better for the future (See: Much faster (hopefully), smaller (mostly) and better PMS builds preview (1.15.0.573-123756e9a)) so the maintainers of the port/pkg or script had time to update (and still due, remember: this is BETA), and it would be very unfair to criticize them to take a bit longer, especially the UpdaterScript maintainer… he took his own time to provide this tool for free and shared its code, It doesn’t seem fair to ask much more than that.
I do think that when we have a public build, both the script and ports/freenas plugin will get updated (the later simply depends on the port update anyway), maybe even before that, this as been the case in the past and even if it does take a bit longer, I still think we should be thankful for it.
Now with all that said, and without promising anything I do know its being discussed that we could perhaps (special now with the new system) provide a more direct way of updating on freebsd (like with do for other systems, i.e. with linux .deb/.rpm etc that allow u to install directly). Right now we provide the tarball that is used in the port, but this can’t be installed directly with a simple command, perhaps we could take ownership of the port it self, or something of the sort. I personally would like to see that happen but as I said can’t really promise anything as so far this was simply up for discussion, so It might never happen, but 
