Apostates reminds me bit of military dissertation.
Muhammad did say Islam will perish. Plus, I thought there is nothing In the Quran that says you should be killed for leaving Islam.
But you're not discussing 'the Quran', but rather adoption of parts of Shariah law. Which certainly does/can include interpretive additions.
In terms of apostasy, I'm not even talking about purely 'killing', but any segregation based on religious belief/non-belief.
Similarly around other areas, such as the weight given to verbal evidence from women.
Ultimately, you're advocating taking some/all of a religiously based legal system and adding it to existing criminal legal systems. We need more information on how that would work, what you're adding, etc, if we are to give meaningful responses.