from what ive heard from scholars and some ive even asked, the justification they give for keeping green dome is 'the dome is not on drop of the grave, it is on top of the house of aisha رضي الله عنه which also has the roof of the masjid over it.eg there are two structures beneath the dome'
as far as im concerned this is a very silly and cop out answer, it reminds me of the 'islamic' mortages where you just change the name and package it differencet but essentially offer same thing. the green dome serves same purpose as any other shrine so what difference does it make if its directly above grave or if there are other structures beneath it?
also i think deobandis defend it to try take some of the brealiws claim of being the loves of rasoolullah . deos and brealwis can sing forever naats about madinah yet hardly any if any at all about makkah and al aqsa.
things like this is best to be honest and balance. on one extreme you have extreme salafi scum who i know some utter filth like ' we should dig the prophet and his companions out and move them to baqi' may Allah disable the hands and break the backs of any fool who dares to do this. the other extreme is in the name of being 'aashiq e rasool' you turn a blind eye to the wrong stuff that takes place. may Allah bless the ottomans and that but end of the day hadith is clear about building shrines we cant let this pass cos its the prophets grave.
finally cos of the fame the green dome has i cant really see it ever going. if im not mistaken the domes been white,blue and another colour before being painted green, infact its been green for less time than it was white and blue but green is the msot famous due to advancement in technology. nearly every single muslim even those who regard themselves as liberals, seculurists or even kaafir qadiyanis have all seen picture of green dome. i too must say having been there a few times alhamdulillah if i saw the dome a different colour its be little confused and if it was totally removed id probably be screatching my head and asking if iv come to the right place. its almost synonymous with madinah and masjid e nabawi.