When going forward and replace globals with use of ContextSource::getConfig(), than the global $wgVersion must be deprecated, because it is not a changable config you should set in your LocalSettings.php
I don't think this [$wgVersion] is considered a configuration variable. I'm not sure if we have a policy for this sort of thing, but the way I usually try to differentiate between config and non-config globals (such as wgRequest), is to think whether it would be editable from a database-based Config subclass.
With that, I think wgVersion would not be in that category. Rather, I would expect it to become a constant.