It's easy to put too much weight on that Area51 group of stats. It was devised, years ago, as a proxy for a site's progress in developing an expert community with a substantial audience.
And like any proxy, it has its problems. The proxy is not the target. If it was the target, it wouldn't be a proxy at all. The two are not equivalent, and that means that there will be times when they diverge. It's easy to focus on the proxy, because it's a simpler thing to grasp and to measure than the target - that's its job, after all. But focusing on the proxy is a mistake: it's the target itself that matters.
The target is to build an expert community with a substantial audience.
Earth Science is, as far as I can tell, doing really well at building an expert community with a substantial audience. The proxy is, in part, out of step with the target here.
So the site is not unhealthy. Far from it, it's pretty healthy as young beta sites go. There's activity on the main site, here on meta, and on chat. There are good questions coming through, some great answers, lots of regulars, and lots of new posters coming in all the time.