Yes, many things got converted from the pagan ways into Christianity to help with the conversion – ie. Churches built on sacred ground; at Yule the giving of presents, which was converted to represent the birth of Jesus & the wisemen bringing gifts (even though he was not born on Dec 25th – most likely in the summer months). The tradition of Xmas gift-giving, decorating a tree, feasting, singing, etc are all rooted in pagan traditions. Initially even some Druids joined the Church and became Priests, (incorporating some of the new ways with the old), which helped with the conversion from paganry to Christianity (and as time went by, many of the pagan ways dropped). Easter is also based on an ancient pagan festival celebrating the Spring Equinox. The term Easter was the name of the goddess Eostre. The Easter Bunny and Easter eggs are pagan traditions as symbols of fertility (new life/Spring). It is likely that the Church tried to stomp out these ancient traditions, but in the end they got incorporated.
In reference to baptism – Many Church Leaders today use a doll as a model to show children at schools how a baptism is done.
It could be that in the past, in the same way, that girls had been taught about baptism by parents (or watched one being performed), and so wished to bless their own doll in the same way, and so dipped the doll into a holy well for spiritual protection – only guessing though !