That's like asking why the super mutants in Fallout 1 killed the vault dwellers in the cutscene rather than capturing them. Because it looks way more dramatic that way. Really, that's all I can think of.
Alternately, it could have been a show of force. Vault 13 supposedly housed a lot of people (it had a capacity of close to 1000 iirc, I don't recall if Fallout 2 gave a population number) so killing a handful of people in order to show you mean business would probably be a good tactic. The vault still had more than enough bodies to serve the Enclave's purpose.
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Muwahahahahahahaha!!!What do you mean evil laugh!? This is how I always laugh!
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