When the Tau'ri took the Lantean scientists hostage, they expected them to follow the Tau'ri patterns of science vs. military, to in essence still be Tau'ri scientists.
They expected the scientists to not know how to handle a weapon unless they were on a gate team, to follow the Daniel Jackson model of being a civilian scientist and prefer diplomacy to violence. To sit and do nothing with guns pointed at them while they waited for their military to either capitulate or retaliate.
Lantean scientists were not like Tau'ri scientists.
For all that they had mostly been born and raised on Earth, they weren't Tau'ri. All Lanteans had combat lessons unless they were on the injury list, from P90s down to hand to hand and everything in between. All scientists were in the militia which protected Atlantis when threats came to it. And the enemies in their galaxy couldn't be talked around with a bit of diplomacy, not even the human ones. The Lantean scientists had adapted to their circumstances, just as they adapted to the latest situation and in short time had the Tau'ri military on their knees, hands on their heads, with pistols pointed at them.
Pegasus was a harsher galaxy than the Milky Way, and the Tau'ri finally learned that lesson.
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