In the intro,a group of enclave soldiers killed a group of vault dwellers.But why though?they arent "muties" and probably have never been affected by radiation.

Because they were storming it I think, taking out the people at the entrance so they could capture the people inside for experiments with FEV; they needed pure people, unaffected by the hazards and radiation of the wastelands

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.