This is something bugged with your game then; this is what should happen.
A) You start the game and harvest the amount of money requirement (no clicks needed).
B) you get the Sonic tanks and destroy the windtraps
C) Imperials get angry at you for doing that and then start with the attacks.
And then only after the "C" part it's done, he will start launching attacks, but no before that.
Did you play any modded campaign recently? because maybe my trigger it's "certain unit/building exist" but due you using a modded version, that unit/building arealdy exist (or don't) and everything trigger before expected.
If you want to check this is the teaser I did for the campaign, I did move a bit the harversters (exploring a bit the area) for the sake of the video, but you can see how I am just calming doing my thing. https://www.youtube.com/watch?v=wwE-hAQqKxo
Just in case I recently downloaded the mission and applied/loaded with the mission launcher.
Nothing wrong happened to me (That's the MCV landing).
Harvesting the quota, doing the windtrap thing, receaving the MCV, no enemy unit on sight.
In fact, the enemy it's made to be passive, and will actually waits until you fullfill the windtrap goal, when you do that, you get a MCV. When you deploy the MCV, the enemy can start producing units, and only when the siege tank it's produced (which will take some time as the AI will build other units befre), an enemy wave will trigger and launch a attack.
It's true that you only have low tech to protect against combat tanks and so on, but it's just that, he is passive until you do that job (or if you let the game running for... dunno, maybe 3 hours, then he may launch an attack on you).
Just be sure that you copied the file "tiledata.bin" provied (although I don't think this has anything to do with it), which path it's "data/bin", but if you already did, then you may need to rever whatever change was done on the game.
Here, these are the usual 4 files that gets modded depending on the campaign, this upload are the originals I have as a back up. Template Original.rar
They are in the folder "data/bin". So try to overwrite them. This should revert the game to the vanilla state and try again the mission.
And again, the battle shouldn't ever start not until a MCV it's delivered, and even then, the AI will take some time to arrive (so your Sonic tanks have enough time to come back, you can build a second ref and barracks and group a decent amount of infantry/troopers to protect yourself).
Even storywise you are the neutral faction, Imperials are not the attackers, you are the one that "attacked" a windtrap the emperor wanted and then retaliate because of that action.