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I had thought that previous laws were superseded by later laws.

only if later laws invalidate them, which isn't true in this case at all. Since the new law doesn't cover religious belief, but is intended to protect homosexuals, it's completely invalid in this respect and only the EEO laws apply.
Since it was passed by Congress, I don't see how it is invalid unless it is shown to be unconstitutional. Do you think that would happen?

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I guess you are also assuming that there are not any Methodists or other Christians who would like to teach evolution.
I don't see how this is related to EEO.

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Quite a number of lawsuits have been brought for various related reasons.

Things are changing quite rapidly anyway, the federal gov now places all sorts of requirements and restrictions on religious organizations for claiming their tax exmept status too. Religious freedom is becoming a thing of the past. But Jesus did tell us to pay the taxes so we'll see who bends or breaks as a result of those requirements I guess. All the churches have to do is pay the taxes to be free of the requiements, perhaps God is judging whether they love him or mammon more.
That is an interesting position to take concerning your religion. It makes a bit of sense though. Those rules are to keep everyone from claiming that they are a religion. You might note that atheism is not tax exempt and neither is evolution belief.

A faith that connot survive collision with the truth is not worth many regrets. -- Arthur C. Clarke