Its clear that in no way does the fact that Isa (sa) was not killed or crucified suggest that he is alive in heaven. This same ayah can apply to even the Prophet Muhammad (sa) who was neither killed nor crucified and was also raised. This applies to many prophets and many
righteous people who have died. They were neither killed nor crucified & were indeed raised by Allah, who is Al-Rafi, the One Who Exalts - The word rafa’a, whenever it is used for a human beings always refers to the elevation of the status on whom Allah has caused his exaltation
We see this clearly from the Qur’an, in many examples. Allah States in regards to Prophet Idris (as) that he was raised too but you dont believe Idris (as) is alive in heaven although the same word is attributed to him. 
Here are more examples from the Qur’an that every single time, Allah speaks of causing rafa’a on a human being, it is spiritual exaltation.
The verses which sepak of Isa (as) death are these.
