I ran into the same issue as the original poster. It's frustrating, and all this talk about how much siege frigates are setting back the empire that uses them to rush with, are frankly bull.
What's 'bull' about it is that those siege frigates are not sacrificed in the strategy. Once they encounter something that can actually destroy them, they either flee or move onto the next planet and commence more bombing. They can keep wrecking up sh*t.
I didn't actually lose my homeworld this way, though the population was knocked down to zero. My two colonies were nixed though, despite the enemy fielding no actual combat ships. They knocked down my homeworld to 0 pop with 4 siege frigates, then sent 4 more siege frigates. I had about 8 combat frigates and a front-line battleship but I wasn't able to pump out enough damage.
All my colonies had a fighter hangar(bombers) and a gauss cannon. In one case the siegers were within range of the gauss cannon, but it made no difference. This was very early in the game, and this, combined with early scouting of the enemy homeworld, gave me the strong sense that the standard AI was cheating its ass off. Or at least, had a perfect build order.
Considering the expense of placing those defenses around all my worlds, I would've been better off just building more ships. If I could've researched and built three carriers that would've been many times more optimal than placing hangar bays. It still wouldn't have stopped the siege-rush from being a runaway success though.
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1) Defences don't cost that much.
2) the TEC and shield their planets
3) if you want to "defend" a planet, get at least 5 gauss turrets, about 2 hangar bays, and a repair station or two.
4) just park a colony frigate nearby. When the planet dies, you instantly recolonize.
This happened to me as well. All I did was stall the computer enough to jump my forces in and destroy their fleet. Overall it really doesn't effectively do anything.