In the very next chapter of Exodus, God makes the commandment not to kill clear.
Exo 21:12 He that smiteth a man, so that he die, shall be surely put to death. 13 And if a man lie not in wait, but God deliver him into his hand; then I will appoint thee a place whither he shall flee. 14 But if a man come presumptuously upon his neighbour, to slay him with guile; thou shalt take him from mine altar, that he may die. 15 And he that smiteth his father, or his mother, shall be surely put to death.
Note that neither the word "kill" or "murder" is used, but the meaning is clear. These verses show the commandment not to kill means to kill with intent or premeditation.
There are other verses as well that make the meaning of Exodus 20:13 clear. The Hebrews were not confused by this, only those who try to undermine the scriptures.
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