Firstly, I agree in entirity with armughal about the "being raised," issue. It is an article of faith that all will one day rise to answer for their deeds and in this case, Jesus speaks of the same day of judgement.
Regarding waffahu in chapter 24:39, it is not translated as death as fawaffahoo is the word used in the conect and not waffa, which is a completely different word.
There has been little other attempt to refute that Isa has not died, apart from this one single line. Other points have been talked about. One of them is the "raising of Isa" (as) for which the arabic verse often quoted is "rafaa" which in my first post is translated as "raising to myself. However, let me show you other translations of the same verse.
From Islamicity:
**Tilka alrrusulu faddalna baAAdahum AAala baAAdin minhum man kallama Allahu warafaAAa baAAdahum darajatin waatayna AAeesa ibna maryama albayyinati waayyadnahu biroohi alqudusi walaw shaa Allahu ma iqtatala allatheena min baAAdihim min baAAdi ma jaathumu albayyinatu walakini ikhtalafoo faminhum man amana waminhum man kafara walaw shaa Allahu ma iqtataloo walakinna Allaha yafAAalu ma yureedu
2:253 Those apostles We endowed with gifts, some above others: To one of them Allah spoke; others He raised to degrees (of honour); to Jesus the son of Mary We gave clear (Signs), and strengthened him with the holy spirit. If Allah had so willed, succeeding generations would not have fought among each other, after clear (Signs) had come to them, but they (chose) to wrangle, some believing and others rejecting. If Allah had so willed, they would not have fought each other; but Allah Fulfilleth His plan. **
Here, it is talked about as raising of status, just as the status of Isa (as) was raised.
**Wahuwa allathee jaAAalakum khalaifa alardi warafaAAa[/y] baAAdakum fawqa baAAdin darajatin liyabluwakum fee ma atakum inna rabbaka sareeAAu alAAiqabi wainnahu laghafoorun raheemun
6:165 It is He Who hath made you (His) agents, inheritors of the earth: He hath raised you in ranks, some above others: that He may try you in the gifts He hath given you: for thy Lord is quick in punishment: yet He is indeed Oft-forgiving, Most Merciful. **
Here, it is clearly shown, that being raised is in the sense of being raised in rank.
**Walaw shina larafaAAnahu biha walakinnahu akhlada ila alardi waittabaAAa hawahu famathaluhu kamathali alkalbi in tahmil AAalayhi yalhath aw tatrukhu yalhath thalika mathalu alqawmi allatheena kaththaboo biayatina faoqsusi alqasasa laAAallahum yatafakkaroona
7:176 If it had been Our will, We should have elevated him with Our signs; but he inclined to the earth, and followed his own vain desires. His similitude is that of a dog: if you attack him, he lolls out his tongue, or if you leave him alone, he (still) lolls out his tongue. That is the similitude of those who reject Our signs; So relate the story; perchance they may reflect. **
Again, this is raising in status.
**WarafaAAa abawayhi AAala alAAarshi wakharroo lahu sujjadan waqala ya abati hatha taweelu ruyaya min qablu qad jaAAalaha rabbee haqqan waqad ahsana bee ith akhrajanee mina alssijni wajaa bikum mina albadwi min baAAdi an nazagha alshshaytanu baynee wabayna ikhwatee inna rabbee lateefun lima yashao innahu huwa alAAaleemu alhakeemu
12:100 And he raised his parents high on the throne (of dignity), and they fell down in prostration, (all) before him. He said: "O my father! this is the fulfilment of my vision of old! Allah hath made it come true! He was indeed good to me when He took me out of prison and brought you (all here) out of the desert, (even) after Satan had sown enmity between me and my brothers. Verily my Lord understandeth best the mysteries of all that He planneth to do, for verily He is full of knowledge and wisdom. **
Needs no explanation.
**WarafaAAna laka thikraka
94:4 And raised high the esteem (in which) thou (art held)? **
All other instances in this are relating to raising the heavens to their position, which are fixed.
Wasalam,
Hasee