The biggest problem that Muslims face is poverty. I am familiar with this situation in several cities, where Muslim orphans or children from poor Muslim families are given to Christian orphanages, where they are then raised as Christians. This happens to the poor Hindus as well.
I don't blame the Christian missionaries or the Muslim parents/orphans. If Muslims want to avoid this situation, then they need to provide for the poorer sections of society the same way the Christians do.
The Jamaat-e-Islami Hind is now actively setting up schools and orphanages to cater to this section of society. And thankfully, they are not setting it up as a Madrassa. It is a boarding school affiliated and based on the central or state board, with some Islamic classes.