To quote the exchange (from the Scream Script):
RANDY: Jesus, Sid. We gotta get out of here.
Sidney throws the gun forward.
SIDNEY: Stop. Right there.
RANDY: Don't shoot. It's me.
SIDNEY: Don't come any closer.
RANDY: Listen to me, Sid. I found Tatum. She's
dead, she's been killed...I think Stu did
He takes a step forward when another VOICE SPEAKS UP.
VOICE: Don't believe him, Sid.
Sidney spins around to see Stu moving up the walk.
STU: He's lying. He killed Tatum. And Billy.
Stu moves closer to Sidney.
SIDNEY: Stay away.
She aims the gun in his direction.
STU: His movie nut mind has snapped, Sid.
He's gone psycho.
RANDY: Don't listen to him. It's him. He's the
STU: Come on, Sid. Give me the gun.
RANDY: No, Sid.
SIDNEY: Fuck you both.
So at this stage in the movie, Sid has witnessed her boyfriend (seemingly!) being killed, Kenny killed, a host of other deaths and terror is gripping her.
Then, in the midst of it, two of her friends, either one of which fits the profile of killer perfectly, show up and tell her to give them her gun. She realises it's a choice between trusting one of them and making the wrong choice or trusting herself and her own instincts. She chooses to do that and shuts them both out of the house, keeping the gun for herself.
Your point is very valid though. She certainly saw the killer in the house. But it's highly unlikely she was thinking logically at this point, given all that had happened.