All that was well before Martin Luther broke off and created the Lutheran church, which probably inadvertently adopted the Pagan elements. You also see undertones of Paganism in other religions as well.
I am married to a Lutheran and have permitted my children to be raised in their dad's church, so I am very familiar with that denomination. Martin Luther had a lot to do with inventing or at least perpetuating the Christmas tree. I guess he must have loved them himself. The story goes that he was walking home on a wintry night and was enchanted by the vision of the stars sparkling through the branches of the trees in the forest. So he introduced the custom of lighting the tree with candles inside the home, to emulate the stars through the tree branches. And of course the whole idea of the evergreen in the dead of winter was supposed to symbolize Christ's eternal life, and the stars were to represent the light Christ brought into the world. Obviously this was some kind of re-purposing of Druidical tree-worship, although Luther lived a very long time after the Druids. So I guess the custom of bringing evergreens indoors must have survived in that part of Germany. The English didn't use Christmas trees until after Queen Victoria married her German Prince, and he started using them for the royal family. Before that, the English had gone in for holly, ivy, and mistletoe--pagan reminiscences all. And of course, the Puritans of the 17th century had made it illegal to celebrate Christmas in England, because of all the pagan associations of the holiday. Consequently it wasn't all that big in the American colonies either, at first.
The Yule log, which is mentioned in certain English Christmas carols, was also of pagan origin. I believe it is still an important part of the Christmas celebrations in Scandinavia.
As for Halloween--it is my understanding that Samhain was the biggest festival of pre-Christian Ireland (and I guess the Celts in other parts of Britain, France, etc.). Since it involved some sort of belief that spirits of the recently dead were still walking the earth at that time, the church moved its "All Saints" holiday from May to November, trying to co-opt Samhain. The trouble is, All Saints is sort of solemn and not really much fun. Samhain was tons of fun. So the peasants never really gave it up. They just allowed it to be incorporated into the three-day church observance of All Saints' Eve, All Saints, & All Souls.
Although the Puritans didn't celebrate Christmas, nor did they observe any type of saints' days, they did have harvest festivals. That is where our Thanksgiving came from. I suppose it is just the most natural thing in the world to have a feast or celebration when your harvest is in.