My thanks for all the comments on the previous post.
To clear up some points. My point in note four has already been discussed Dr. Isadore Twersky's book on the Yad in the chapter on Law and Philosophy. David Guttman pointed out that in Shemonah Perakim the Rambam translates Hakol B'yedei Shamayim as Tivo Shel Olam as well which would strengthen my point.
The first difficulty on this Rambam is that the “simple” interpretation of the Mishna is that a fetus does not have the status of a life (as Rashi explain). This is supported by the wording “her life precedes his” which implies that a fetus does not have the status of a full life. The second difficulty (that we shall discuss soon) strengthened the difficulty, for why did the Rambam choose a difficult explanation that is not fully supported by the Talmud.
David Guttman suggested that the Rambam is forced into this based on his position that it is forbidden to “heal” oneself by transgressing the three central sins. R’ Unterman zt”l (Noam Vol. 7- perhaps in Shevet M’ Yehuda as well?) makes a similar point. Therefore the Rambam could not permit a transgression against murder without the special heter of Rodef. This point in and of itself is insufficient. For the view of Rashi is that a fetus is not a life at all and therefore the prohibition against murder is irrelevant to our case.
Further, R’ Zevin (review of Rambam and Mechilta D’Rashbi) has differentiated between an argument and a source. That is one can convincingly argue that the Rambam was forced to hold a certain position based on a “L’Shitosoi” and the like but we need a definite source for this position. The Rambam almost never wrote Halachos without a source. Each Halacha is based on a particular passage in the Talmud or more rarely on a Geonic ruling. We need to find a Talmudic source that applies Rodef to this particular case.
In truth, the source for this Rambam is very simple. So very simple that I am astounded that none of the many great Geonim that have studied this Rambam appear to have noticed this explanation.
R’ Kappach has stressed the importance of studying the Sugya without learning any of the commentaries. Once you learn a Sugya according to Rashi’s explanation you internalize to an extent that you cannot see any other understanding of the Sugya. This prevents you from recognising alternative understandings of the Sugya such as the Rambam may have had .
The Gemara finds R’ Hunna’s statement (on the issue of Rodef) difficult because it contradicts the Mishna in Oholus. The implicit assumption of the Gemara in comparing these two sources is that the Mishna in Oholus also involves a question of Rodef. The Gemara never retracts that comparison.
Rather, the Gemara says that the end of that Mishna is not difficult because “Shmaya Ka’Radfi Loh”. That is, this part of the Mishna refers to a different type of Rodef . The first part of the Mishna would remain with the standard heter of Rodef.
This is clearly the Kesef Mishna's understanding of the Rambam as well. This is why he quotes the entire sugya as a source for this Rambam. Otherwise he should have divided the Mishna in Oholos for the first part of the Rambam and the end of the sugya for the second part of the Rambam. See there and you will see it is like I say. (He rules like this Rambam in SA CM 425)
 My thanks to Dr. Shapiro for this reference.
 The one commentary that should be focused on is Rabbenu Chananel. For the Rambam seemed to have studied the Gemara using this commentary.
 Note that even in the Gemara's answer the key word "Rodef" (Radfi) is still used.