It should be a step in the right direction in the long term. The commercial Unix world (Solaris, HP-UX, AIX, OS X, and others) has had the base system under packaging for quite some time, and it works quite nicely. Being able to add/remove/list/verify/patch/etc base components and packages under a common set of tools is really quite nice. With suitable granularity, it can allow things like replacing base services/daemons (e.g. BIND, Sendmail, NTP, etc) with newer/alternate packages much more cleanly than the 10.x status quo; including just as easily reverting to the base packages. Theoretically, no more messy situations of duplicate functionality being simultaneously installed in base and /usr/local; with corresponding confusion about which version of command line tools you are getting in each shell, etc.
There's no fundamental reason why a problem with a port should disrupt the base packages, if the implementation is done correctly, unless the user does something like --force --live-dangerously --yes-really --just-do-it
. Now, I'm not saying that pkg necessarily has that level of safety today (I don't know for sure just where it's at), only that there's no fundamental reason why it can't be made as safe as that in terms of preventing base and ports easily having a bad collision.