It was their homeworld. Holding the bulk of their people. *Most if not all of their women stay on the planet, as is custom to their hegemony. (*I will look for the exact location of that info, for reference. I remember it somewhere, but if I am incorrect, I will retract this statement.)
When they blew that relay, the initial blast killed 300,000. Yes. Not a lot in the grand scheme. But it cut off any escape for the rest of the batarians still on the planet when the reapers rolled through. Leaving the other possible millions to their fates.
If they were on that planet when the reapers came, there was no escape. Meaning if the source I found is correct, that means all the women who were on the planet, were by all rights turned into husks, along with every one else. Take away the women, you cut off natural reproduction.
Any remaining batarians will die out from age or other things, and the race as a whole will be gone.
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Yes, it may be a lie. I get that. Hopefully it is, since it is most likely canon that the destroy ending took place.
However, you don't know that when you're making the choice.
Shepard has to take everything that damn space bastard says at face value. If he says the catalyst will kill the geth and other synthetics, then in my mind, I can't justify it by saying, "I bet he's bluffing." He's the only one with answers. What he says is what is truth, at least at that point, because we soon see that there is more to this than we had known, and that this thing had been alive for countless millennia, knowing more than we as a race ever will.
As harsh as it sounds, if you choose destroy, knowing what the catalyst told you, you accepted the geth's demise as a reasonable cost for a blank slate.