Historically, this sort of gesture has actually hamstrung the cause of the gospel in the Muslim world by exacerbating the enmity against those considering baptism, isolating converts from their natural social network, and making the price of conversion the loss of all family (including children) and friendship ties. The result: only the already marginalized became Christians and many didn't go the distance because the social isolation was too terrible to bear. The breakthrough happened when Christians stopped demanding individuals convert in a way that doomed them to isolation and started to work with whole families, tribes, and people groups.
With all due respect to her (and I really do respect her ministry, may God prosper it!), I think she is perhaps missing a couple of things which I want to point out. There is in the mission field of the Middle East and North Africa (MENA) generally only the possibility of private baptism. A minister, the convert, and perhaps some people from the local church, if there is such a thing. A de facto baptism open to the public and where it is known in advance that one of the candidates is a Muslim is probably impossible, except maybe in Lebanon. So really comparing Rome with any of those cities is not sensible.
But will this bring persecution on the Christians in MENA? Well, the honest answer is they already have it. Living fearfully and sheepishly and hiding our lights under baskets is not the way of the Kingdom of God. Good for el papa. Let your light shine before man. Allam is a Christian now, and a son of the Catholic church. That is good news and we are to shout it from roof tops if at all possible. In Rome it is still, for now, possible. The day is coming when it may not be...
Christians in MENA will indeed live with this for years. They will live with the image of the best know Christian in the world baptizing a Muslim. It will give them hope. It will encourage other Muslims to convert. It will, in a few Muslims' minds, occasion the question, "What if I left?" Most of them have never even considered the possibility. Many of them don't even know that people DO leave Islam.
This is great news for the Catholic Church as well as the mission to Muslims. Muslims respect the Catholic Church and the pope because he is powerful. That is a language that they can understand. They know that he holds more sway around the world Christians than does any single person in Islam. They know he has a country of his own. They know his office is very ancient. These things, to the Muslim mind, and specifically to the Muslim Arab mind are often attractive. Becoming a non-denominational Christian with no clear affinity or relation to anyone else is not always appealing to a Muslim considering conversion.
So yes, will there be persecution? Of course, but at least this time it will be for a good and glorious reason: the public confession of faith of a Muslim hajji in the best-known church in the world on the holiest day of the year by that city's bishop.
Persecution will come, and marginalization from families is almost unavoidable, dear sister. Jesus knew this well--that his message would divide families, which is why he promised that anyone who left wife or children or brothers for him would receive ten thousands times more in the next life, and this life. Those thousands upon thousands of new brothers and sisters are me and you. Amen.
(PS: I don't see how this baptism of Allam means that the church is not working with peoples and tribes...)