Salamun Alaikum.
The Quran was not sent down with or without an ‘alif’. This is a mute question from a ‘qiraat’ (recitation) perspective.
God did not reveal the Quran on tablets with written words like the Torah.
The Quran was sent down as a ‘qiraat’ (recitation) which was then / afterwards taken down by scribes to represent the qiraat. It is the ‘qiraat’ which is important and how it is pronounced today.
You can write it in English if you want as long as the English correctly represents the ‘qiraat’ and allows you to extract the correct meaning!
If you want to know how the Quran was taken down by the earliest scribes in the earliest manuscripts, then that is a different matter. The original manuscripts only had ‘rasms’ (i.e. without vowelling and diacritical marks etc). The markings were only introduced later and again, as an aid only.
However, if it was written ‘he said’ (qala) in some manuscripts and then ‘qalat’ (she said) in another, then one would have a cause for concern. Or if it said, we sent 2 messengers and strengthened with a third (Yaseen - 36:13) and in another it said “we sent 8 messengers and strengthened with a 9th”, then we would have a serious problem!
It is the majority ‘recitation’ which has propagated by consensus and not a particular script and whether something has an ‘alif’ or not. With respect, these are all mute questions in the context of the overall message which God has protected. God did not say He will protect whether something is written with an ‘alif’ or not. The scripts were only / simply an aid to memory which kept the message stable and without corruption of the Divine message.
I hope that helps, God willing.
Joseph.