Not at all, I just don't see how there would be time for "atrocities" if all planets are hit simultaneously with overwhelming force, arriving under (personal) cloaks, like a squad of assasin droids for each Jaffa, and a battleship for each death glider.
It didn't sound like the situation involved standing orders to detonate suicide nukes at the first sign of trouble - even without considering what SG-1 has seen. Did Ra's forces massacre all of his slaves after he was killed?
And that's the problem.
You're trying to fit the Empire into a tiny little SG-1 shaped box.
No.
This is an Empire that openly decries the Goa'uld culture, and when capturing a world puts extensive effort to undo generations of cultural conditioning and it was working. They were levering propaganda against them in surprisingly effective measures. You know what that does?
It leads to revolts because the people are being shown that the Goa'uld suck wang and that there is another force out there capable of beating them.
Revolts lead to Goa'uld repressing those revolts.
That, combined with the Emperor focusing on the people themselves - saving them from the Goa'uld and having that be his open public motive - led to that great and wonderful thing = spite. Angry, furious spite. So yeah they started burning worlds, and yeah they now have standing orders for it.
Oh, sure, the Empire would win that fight. Of course they'd overwhelm them at the end of that like you seem to want. But not before too many Goa'uld vessels under now Standing Orders from their Gods burned the worlds below with their absolutely effective planetary bombardment weaponry.
Because you know how many worlds is too many?
One.
And it would be more than one.
Not to mention the fact that the Empire was also busy fighting a bunch of other threats like say Replicators and Wraith and Ori - which doesn't even get into the intense amount of work it takes at all to reverse all the psychological damage that the Goa'uld inflicted on all those under the whip.
So yeah. You are exactly wrong. There now are standing orders for massacring. Because the Empire pushed too hard, and too fast, and was too obvious about its intentions. The Emperor fucked up.
The Empire of Wu is fucked up in plenty of ways.
Guess what!
Shit ain't fixed with a snap of fingers here.
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