If you think that it might currently be too easy to get enough ancient constructions to stop aether rift growth, have you considered adding some separate, more powerful kind of anomaly feature that, when worked by a colony, actually INCREASES the rate at which aether rifts expand?
Would act in some sort of risk vs reward way and make invaders stay relevant in the later game. It would require the player to strike some sort of balance between (weaker, but saver) ancient constructs and these (more powerful, but more dangerous) other anomalies, unless the player doesn't care about throwing the galaxy into chaos (literally).