It is nice to see a Muslim actually commenting on the case at all, but al-Marayati's article is just another example of the unproductive approach moderate Muslims are taking towards the problematic elements of Islamic theology and law.
Of most concern is Marayati's claim that the Islamic death sentence for apostasy was actually originally conceived of as only applying to cases of treason. Marayati will have a lot of trouble making this one stick. An authoritative hadith attributed to Muhammad himself has the Prophet saying: "Whoever changes his Islamic religion, then kill him." (Sahih Bukhari v.9, b.88, no.6922, and others) He doesn't say, "Whoever changes sides and fights against a Muslim army, then kill him." The command is based solely on changing one's religion.
Similarly, if we look at Islamic law itself, it's the same story. The earliest ruling I know of on apostasy by an Islamic jurist was that of Malik bin Anas (d.712), the founder of the Maliki school of jurisprudence, who said:
“As far as we can understand this command of the prophet [in the hadith above] means that the person who leaves Islam to follow another way, but conceals his kufr and continues to manifest Islamic belief...should be executed after his guilt has been established. He should not be asked to repent because the repentance of such persons cannot be trusted. But the person who has left Islam and publicly chooses to follow another way should be requested to repent. If he repents, good. Otherwise, he should be executed.”
By "leaving Islam", Malik meant specifically (in his own words) kufr, which means unbelief, not treason.
Al-Marayati also gullibly reproduces Rifqa's father's insistence that he doesn't want to kill her, and is quite happy to have her come back home and live with them as a Christian. Really now, does Marayati honestly think that if the father does want to kill her, he would say so in public?