Irrespective of other cases and regions, Russia doesn't have any more of a claim to Estonia, Latvia, and Lithuania than Germany, Poland, Sweden, or Denmark have (all these coutries have had control over parts of the region in the past). Any Russian attempt to seize any part of these countries, be it via a "loyalist uprising" or a straightforward invasion, is no more justified than, say, the US invading, and seizing parts of, Canada on some pretext. Or, say, Britain invading Spain.
NATO and EU are far from ideal, but membership in these organizations in voluntary and there are actual benefits to them. If Estonia joins the EU, it doesn't mean that a garrison of German and French settlers will be installed to ensure proper conduct, and that henceforth that "minority" will demand more and more privileges. That's the difference.