I don't buy the pre-programming thing. Notice Rabbi Shlomo Kruger, who advocates it, correctly says that if this is the case then it is not to be considered a miracle. I would not call this position atheism, but "theism light" since it shies away from believing in miracles. The Torah says that the parting of the waters happened when Moses stretched his staff over the sea, which is the time that G-d intervened in nature and caused the waters to part. A lot of G-d's miracles are also dependent on free will. In Jeremiah it tells us that G-d can change His plans on whether to fulfill prophecies of reward or punishment based on people's behavior. And what about the times that G-d spoke to Moses? If it was actually G-d's voice then it would be G-d intervening at that time in history and not a pre-destined audio recording. G-d couldn't speak to the prophets if He was currently just a bystander. Therefore it is G-d intervening, not pre-destining, in nature that causes miracles to happen. However, I can see how those with atheistic tendencies might buy into this one because it reduces G-d to a less active role which is the next step to atheism.
It is not only Rabbi Kruger who says this. It comes from the sages...It has ABSOLUTELY NOTHING to do with Atheism, and as you can see Rambam subscribed to this particular understanding...
As a matter of fact the Pirkie Avot {Ethics of the Fathers} a Talmudic tract, states the following:
Ten things were created at twilight of Shabbat eve. These are: the mouth of the earth [that swallowed Korach]; the mouth of [Miriam's] well; the mouth of [Balaam's] donkey; the rainbow; the manna; [Moses'] staff; the shamir; the writing, the inscription and the tablets [of the Ten Commandments]. Some say also the burial place of Moshe and the ram of our father Avraham. And some say also the spirits of destruction as well as the original tongs, for tongs are made with tongs. (Avot 5:6)
http://blog.webyeshiva.org/teachers-contributions/insights-in-pirkei-avot-the-final-moments-of-creationWhat commonality unites this disparate list and why were these things formed at the very end of the six days of creation? Many of the listed items refer to miraculous events and the previous two mishnayot in Avot catalogue miracles; thus, we may have another enumeration of divinely inspired changes in nature. Rambam offers such an interpretation while reading the mishnah in light of his strong endorsement of the stability of the natural order. Divine perfection entails making a world which does not require constant tinkering at later sages. In fact, subsequent deviations from the regularity of nature were all programmed in at the time of creation. That is the implication of G-d creating miraculous elements just before the first Sabbath.
This mishnah does not offer an exhaustive list of biblical miracles; note that the splitting of the sea does not appear. Why focus on these specific miracles?
Rambam explains that other miracles were programmed in during earlier days of creation. For example, the splitting of the sea was planned on the second day of creation when G-d formed the waters. It remains unclear why certain miracles were incorporated early in the six days whereas others were left for the end of process. That some of the listed items, such as the rainbow and Avraham’s ram, do not refer to miraculous events provides another difficulty for Rambam’s interpretation.
In Moreh Nevuchim (2:29), Rambam cites midrashic support for his interpretation. Yalkut Shimoni (Yehoshua 21) states that G-d made a condition with the sea at the time of creation that it would split for the Jewish people at the appropriate moment. Arguably, this conveys the idea that G-d preprogrammed all miracles into the created order.However, Tosafot Yom Tov points out an alternative reading of the midrash. A different midrash (Tanchuma Bereishit) says that G-d made a condition at the time of creation that the world’s survival depends upon the Jews accepting the Torah. That second midrash refers not to miracles but to the purpose of creation. Perhaps the midrashic motif of divine conditions made during beriat olam always suggests something about the telos of creation. If so, the midrash from Yalkut Shimoni says something abut the great significance of keriat yam suf but nothing about the nature of miracles.
Meiri offers an explanation of the mishnah in Avot in which the mishnah enumerates ideas crucial to our worldview. Their inclusion in the six days of creation indicates their ultimate significance. The earth opening alludes to punishment of the wicked while the well of Miriam indicates reward for the righteous. I will not outline his explanations for the entire list here but will suffice with two intriguing aspects. According to Meiri, the burial place of Moshe is significant precisely because we do not know where it is lest it become an object of worship. We certainly acknowledge the greatness of our heroic leaders but we also reject any attempt to attribute divinity to them. Meiri explains that mazikim (translated above as “the spirits of destruction”) refers to the evil inclination, itself a crucial element of the created order. Without the energy and drive generated by the aggressive elements of the human personality, the world could not survive (see Bereishit Rabba 9:7).
Avot certainly serves as guide to Jewish ethics but it may also be a guide to Jewish philosophy. Meiri’s reading gives this mishnah philosophical weight and theological importance.