The captain's upset that she took it upon himself to kill Niels. He hadn't decided yet on what to do with the scumbag, and probably wanted to hold a court-martial aboard ship to properly try, sentence, and then execute the POS. After all, not only was the scum a carrier of the virus, but he was helping the Immunes conduct biowafare against people in safe zones (the contaminated teddy bears).
Dr. Scott will likely be confined to quarters for a while, but when she's needed again (as is likely), the bad feelings the Captain has now will be swept under the rug and that will be that. If the crew had their way, she'd get a medal.