You're probably right from an Aurora-as-video-game perspective: players hate setbacks. Sid Meier's autobiography discusses this: the Civilization team considered implementing a "civil war" game mechanic, but eventually shelved it because most players hated losing their cities. Even Paradox Interactive's grand strategy games, which do feature civil wars and rebellions, tend to make them relatively minor affairs. There's probably some sort of loss-aversion psychology going on here.
On the other hand, I think that random losses are useful from the Aurora-as-storytelling perspective. The only way for the player to experience "The Glorious Liberation of Hiigara" is as the sequel to "The Hiigara Disaster".
I think that a middle ground could be for the Precursors to only launch their ships after winning the ground war (perhaps there could be an escalating series of ground awakening). That way the player can recapture their (mostly) intact colony later.
Or just use Spacemaster to kill the Precursor fleet. Aurora is a single-player game; there's no such thing as cheating.
Difference here is that resources in aurora are limited (well, besides never ending expansion, and perhaps some exploits, if they can be called that).
In Civilization and Paradox games, resources are more about territory controlled, rather than something finite. The only finite thing that player loses there is time.
You can at least prepare for the coming setbacks in PDX games though - like disasters having specific requirements to occur, and to end.
For unhappiness in Civ games, you expand to places with special resources to compensate. Or, use technology and buildings. There are ways to address losses.
But here though... I don't see any clear way to prepare for this, besides amassing a fleet "in case they wake up". And even then they get the drop on you, because they don't suffer a jump shock or it's equivalent.
Or, simply deciding to not bother going to this system to begin with. Which is... arguably questionable game design. The player should be encouraged to explore and expand. Why this should be an exception?
Basically, I would be fine with this challenge, if there were ways for player to address it.
But, I don't see it, hence my concern.EDIT:
And yeah, making fleet appear only after the ground war is won does look like a nice compromise.
EDIT:
At the very least, my suggestions about odd happenings as your excavation teams dig stuff up gives an indicator to player that something is afoot. The player can at least decide to reduce potential loses and evacuate things.
As for the excavator work - perhaps it would be better to have several different outcomes? Like, in terms of ships:
Outcome 1 - excavator team finds the precursor ship intact. They reprogram it, and get it online (if you have population on the world, you also get it crewed).
Outcome 2 - excavator finds a non-functional precursor ship. You get resources/components.
Outcome 3 - excavator team accidentally reactivates precursor ship. Luckily, it suffers a serious malfunction. Spawn a wreck in orbit.
Outcome 3.5 - excavator team accidentally reactivates precursor ship. It suffers a minor malfunction. Spawn a damaged precursor ship in orbit.
Outcome 4 - excavator team accidentally reactivates precursor ship. It is now in orbit and does what is described in this campaign.
Precursor land forces:
Outcome 1 - excavator team finds remains of a precursor army. You get some resources and maybe research points in some places.
Outcome 2 - excavator team accidentally reactivates a small group of precursor forces. Spawn a small group of hostile forces on planet.
Outcome 3 - excavator team accidentally reactivates a precursor group, which in turn reactivates their army. Spawn a large precursor ground force.
I am not sure if player should be allowed to reprogram robot armies..?
