The official 1.5.1 patch went live today and there's a discussion on it in the thread I started for it. To quickly answer your question though, sadly we were not able to get achievements to be awarded retroactively. The best we could do was fix them for new saves started in 1.5.1 release.

If you do not have an economy that you trust will be able to pump out and maintain a fleet capable of beating them, let them make you a thrall or whatever and while you are a thrall or what not focus entirely on making your fleet counter theirs and super large.

Then when the time is right, when they are at war with multiple empires or weakened from another war, fight them for independence. Once secured, take advantage of the cease fire and rove around the galaxy with your giant terror fleet, using your newfound freedom to annihilate and enslave the galaxy.

As the last skulls are stomped beneath the feet of your super soldiers and androids realize that in obsessing over defeating the awakened empire, you have become the same nightmare. Let your people agonize over their newfound evil and lose their will to prosper as your empire falls into obscurity in a small corner of the galaxy and wallow for thousands of years as new little races reach for the stars for the first time around you.

Watch them explore and colonize, watch them fight and trade... until the time comes once more to fire up your shipyards and heed the call once more. Only your species has the right to control the galaxy, soon enough your species will awaken from it's morose limbo and remind the galaxy who it's true rulers are.