They thought Christianity was incompatible with their idea of an unlimited quasi-religious belief in the state which they wanted to implement on the long run, but realized Christian ideas were still too strong within the populace to ignore them. So they did with the Protestant Church in Germany what they did with all other mass institutions too: They attempted to get them on party line. That's why they brought into existence the church of the "German Christians" according to which the old OT Jewish God was not the same God as the NT "Father", but in fact a "desert demon" or even "the devil", and Jesus was made an example for "Arian" bravery and heroism. This main "German Christians" church was supposed to get the Protestants on party line, not vice versa.
Those Protestants who disagreed with the "Germanification" of the Evangelische Kirche formed the Confessing Church, an anti-Nazi Protestant church which disagreed with Nazi ideology.