That wasn't addressed one way or the other, given that we never see S.H.I.E.L.D. fishing the body out of the water. If they wanted to bring her back, they could pull that out, but I think the implication is that she's dead for real noe.
Under the circumstances, I honestly think that lethal force was justified, given Kimura's rap sheet, the fact that she was currently engaged in armed assault and an assassination attempt, and that she couldn't be safely captured (I can also see a case being made that this was a legal S.H.I.E.LD. operation). Whether they should've tried to save Kimura after drowning is another question, IMHO. (There is a difference between legal justice and narrative justice.)
(Also worth noting is that Laura planned to turn herself in after the operation, but Fury was the one who decided to not press charges and let her go).