Let's face it, wiped countries are screwed. They lose their economy, income and the ability to use what they have left.
If a country wipes a nation, then the wiped nation should get dual-citizenship of that country.
That way you share the rewards of your new masters and get to vote in their elections. Conquest = internalising your enemy. If they are politically astute they can make it work. If they are dicks then they absorb rebellion. Either way, it brings a practical spin to merged nations... whether voluntarily or not.
And if multiple countries own your regions, then the citizenship goes to the biggest or all of them to keep it interesting.