The Prophet (p) did not order Abdullah Ibn Sa‘ad Ibn Abi as-Sarḥ to be killed for apostating. Rather, the Hadith and other sources tell us that once he left Islam, he joined the Makkan pagans in war against the Prophet (p).
Narrated Abdullah ibn Abbas: Abdullah ibn Abu Sarh used to write (the revelation) for the Apostle of Allah (p). Satan made him slip, and he joined the polytheists. The Apostle of Allah (p) commanded to kill him on the day of Conquest (of Mecca). Uthman ibn Affan sought protection for him. The Apostle of Allah (p) gave him protection. – (Sunan Abu Dawud Book 39, Number 4345)
Maulana Wahiduddin Khan also comments by saying he joined the polytheists who were the enemy of Prophet Mohammad (p):
Abdullah ibn Sa’d, who had become Muslim and been appointed as a scribe of revelation by the Prophet. He later reneged and joined the disbelievers. After the conquest of Makkah, when he heard that the Prophet had ordered his execution, he took refuge with his milk-brother Uthman. The latter gave him shelter, then took him to the Prophet with a request once again to accept his conversion to Islam. The Prophet remained silent. Then Uthman asked a second time, whereupon the Prophet accepted Abdullah ibn Sa’d’s oath of allegiance. 
Islamic scholar Safi-Ur-Rahman Al-Mubarakpuri states that after he left Islam, he killed some Companions of the Prophet (p). Hence, his blood was declared lawful by the Prophet (p) for what he did. But, he was forgiven later.
“Shedding blood of none of the worst criminals was declared lawful even under the curtains of Al-Ka’bah. Some of them were later pardoned. Abdul-Uzza bin Khatal was found holding on to the curtain of the Ka’bah and was killed. Abdullah bin Abu Sarh had become a Muslim and emigrated, but later left Islam and killed some of the companions.” 
 Muhammad: A Prophet for All Humanity By Maulana Wahiduddin Khan page 327
 Ar-Raheeq Al-Makhtum The Sealed Nectar Biography Of The Noble Prophet [Revised Edition January 2002] By Safi-Ur-Rahman Al-Mubarakpuri page 468