As to the whore of Babylon, there are lots of theories as to what is really meant by this image.
My favourite one is that it is the modern hedonistic civilisation with its emphasis on carnal pleasures and its hostility to Jesus Christ. Modern culture is obviously 'whore-like'. It will be destroyed by the Beast - a totalitarian anti-Christian society. But it is just a hypothesis.
I cannot seriously believe that the Roman Church is 'the whore of Babylon'.
On the other hand, when people speak about 'reconciliation', what do they mean? If they mean peaceful coexistence, joint initiatives in the field of charity, in fighting abortion, in standing up for traditional family values, etc. - this unity is possible and is already a fact in many places.
But if they mean intercommunion or submission of the Orthodox Church to the Pope, this is simply out of the question. There are very serious dogmatic and other differences between Rome and the Orthodox Church. Catholicism and Orthodox Christianity are two different religions and to ignore this fact is to ignore reality.
It is a sad fact that the Roman Church has deviated from the authentic Christian tradition by adopting a whole number of false, human-made dogmas. Until Rome renounces its errors and goes back to the faith of the Seven Ecumenical Councils there can be no 'merger' of the Roman Catholic Church and the Orthodox Church.