I have previously discussed the problem of the Rambam’s "deviations in the Mishnah Torah from the reasons for a particular law given in the Talmud." The most probable explanation lies in the combination of reasons quoted here -
רדיפת הפשט, מסירות לערכים פילוסופיים, ומוכנותו לסמוך על הירושלמי לעומת הבבלי, תכונות שתרמו ליצירת דעותיו המקוריות של הרמב"ם, גם כשאלה חלוקות על דברי חז"ל במקומות שונים. בבואו ליישם נטיות אלה (אשר תיאר בהרחבה) לנידון שלפנינו כותב סייקס:
הרמב"ם הרגיש בפערים בין המקורות לפירושים שניתנו להם, וכתוצאה מכך דחה לעתים את פירושי הגמרא והחזיר עטרה ליושנה, בפרשו את המקור כפשוטו. אחרים לא הרגישו שפערים כאלה קיימים, ולכן לא היתה להם הבעיה הזאת
This explanation would seem to me to be the most correct, and can best be supported from what we know of the Rambam himself. Each case still needs to be viewed individually to decide which particular reason motivated the Rambam to deviate from the accepted reasoning.
The Rambam (Nothing I write here is of any relevance to practical Halacha. I am not authorized to do so and in any event have not had the chance to fully analyse all of the sources.) that I have found most puzzling in this regard is the Rambam in Hilchos Rotzeach 1:9:
אף זו מצות לא תעשה שלא לחוס על נפש הרודף, לפיכך הורו חכמים שהעובר שהיא מקשה לילד מותר לחתוך העובר במעיה בין בסם בין ביד מפני שהוא כרודף אחריה להורגה, ואם משהוציא ראשו אין נוגעין בו שאין דוחין נפש מפני נפש וזהו טבעו של עולם עכ"ל:
The difficulty,as usual, is that the Rambam provides a reason that differs from that of the Talmud:
בסנהדרין דף ע"ב [ע"ב] אמר ר"ה קטן הרודף ניתן להצילו בנפשו וכו', איתיביה ר"ח לר"ה יצא ראשו אין נוגעין בו לפי שאין דוחין נפש מפני נפש ואמאי רודף הוא, שאני התם דמשמיא קא רדפי לה
It would seem clear that according to this Sugya a fetus is not considered a Rodef. Rather the mother's danger is a purely natural occurrence, an "Act of God", and therefore the status of Rodef does not apply here. Permission to abort the fetus is given (as Rashi explains) based on the fact that a fetus simply does not have the status of a full human and therefore there is no prohibition against killing it. This view that the fetus does not have human status is supported by other Talmudic sources .  Although it is certainly forbidden to abort except under severe circumstances this is based on the relatively lighter  prohibition against wasting seed.
Thus it is difficult to understand why the Rambam brings the Rodef status of the fetus into the equation. This view of the Rambam has severe Halachic consequences for according to the Rambam it would be forbidden to abort except in a case of a “clear and present danger” to the life of the mother (when the status of Rodef comes into play) but in a case where for example prenatal testing reveals that the fetus has an unbearable genetic defect that would render its life very difficult, or in a case that would involve a psychological (rather then a physical) danger to the mother it would be forbidden to abort.
I find this Rambam particularly difficult because the Rambam would seem to agree with the reasoning of the Talmud. In the next line the Rambam writes:
ואם משהוציא ראשו אין נוגעין בו שאין דוחין נפש מפני נפש וזהו טבעו של עולם
Here the Rambam refers to the mother’s danger as a natural occurence, clearly agreeing with the simple understanding of the Talmud that there is no human "Rodef" involved. We are left wondering why before the birth does have a “Rodef” status.
We cannot say that the Rambam deviates from the Talmud for any of the reasons mentioned above because it is clear that the Rambam accepts the Talmud’s reasoning thus we must look elsewhere to explain this difficulty in the Rambam.
R’ Moshe Feinstein (Igrot Moshe V. 2 Choshen Misphat No. 69) has an interesting introductory remark on this problem. He writes that since the Raavid, the Kesef Mishna, etc. all passed over this particular Rambam without comment it is clear that they had some simple method of understanding the Rambam and the answer must be clear and simple not involving any complicated casuistry.
The Rambam has provided us with a hint by his opening term - לפיכך - it would seem that there must be some connection between the first part of his statement –
אף זו מצות לא תעשה שלא לחוס על נפש הרודף
and the status of Rodef mentioned in the second part of the statement.
I will try to review the various approaches of the traditional commentaries (in particular the brilliant explanation of R' Chaim Soloveitchik) on this difficult Rambam in a future installment.
 My last attempt to reasearch a difficult Rambam as far as I can is here. My assumption was that with all of the many books written on the Yad over the past millenium it should be easy to gather all the necessary info to resolve almost any specific Halacha. As it happens I was wrong. I did not find what would be (to my mind) as satisfactory resolution. I did notice something interesting. The Rambam mentions the Kutim (Samaritans) only twice in the entire Yad (except for those places where it was changes by the Censor), one of them is his programmatic statement in H. Avodim that Kutim have the status of Gentiles, the other in the Rambam I was working with. In that Halacha there would seem to have been no reason to mention them. The Rambam in his commentary to Mishnayot mentions Kutim in the Mishna dealing with that same Halacha (This is not the first mention of Kutim in the Mishna and I do not know why the Rambam doesn't discuss them in the earlier Mishna in that same chapter.) This would seem to imply some very close connection between his commentary on the Mishna and his arrangement of the Yad.
See for example TB Arachin 7a – that states that a pregnant woman who is sentenced to capital punishment is executed right away. We do not wait for the fetus to be born. Proof that a fetus does not have a status of a “life”. I will expand on this in the next installment.
Cf. the Zohar - which states that this is the most severe sin of all. But see R' Yaakov Emden "Mitpachat Soferim" who disagrees and demonstrates that it is not all that severe.
 Of particular interest is that the Talmud's term - שמיא קרדפי לה is changed by the Rambam to זהו טבעו של עולם. Clearly the Rambam was disturbed by the anthropomorphic expression that "Heaven is Rodef her" and he therefore changed it to the less mystical "this is the way of the world". Clearly there is a greater connection between the Yad and the Morah Nevuchim then one might have imagined. On the Mishna Torah as a "translation" of the Talmud see C. Tchernowitz Toledot HaPosekim V. 1.
The Rambam’s general methodology was far from complicated casuistries in any event.