It's been around for years; it's hardly "new". And I've had problems on literally all machines I've used it on, from segfaults to weird stuff like this. The developer's response has either been non-existent or a disinterested shrug like the above link.
Two years is relatively new for something critical like pkgng. Although it is a bug, there are ways to get around it until a solution is provided. Hardly a reason to do a knee jerk switch to something else, given all other benefits of FreeBSD. But hey, it's your choice.