There's little to choose between OP's two alternatives, so in practice I think the KISS principle dominates (choose the simpler form had eaten, rather than continuous had been eating).
But to the extent that there's an underlying semantic distinction, it's that we prefer had done for "completed" actions, whereas continuous had been doing implies that Past action was "interrupted" before completion, AND/OR it's not the kind of activity that normally has clearly-defined start / end points (chatting with friends, consuming alcoholic drinks, for example).
Personally, I have a slight preference for had eaten in OP's context because I think in terms of those people having eaten a meal together (an activity with fairly obvious start / end points). But someone else might imagine a scenario where the people who arrived earlier have been casually munching their way through snacks and "finger food" for some time, in which case they'd prefer continuous have been eating [nibbles].