My question is: doesn't the ba'al koreh elongate the amen before proceeding to read the Torah, especially in Moroccan sephardi synagogues, isn't that a sin then???
The Gemara (Berachos 47a) says that one who lengthens the pronunciation of his "Amen" merits a longer life, and if he makes it too long he is making a mistake. Compare this with what the Gemara says about someone who pronounces "Amen" too quickly: that his life is shortened. So the first point I would make is that erring on the "too long" side doesn't seem nearly as serious as erring on the "too short" side.
Second, Tosfos (op. cit., DH Kol) explains that the problem with stretching out the pronunciation of Amen is that one no longer hears the word "Amen" clearly. My experience is that the Ba'alei Koreh do not stretch out the "Amen" to the point that it is no longer understandable (granted, I have not had the privilege of davening with a Moroccan Sephardi Kehilah and hearing their Ba'al Koreh).
The Talmud Yerushalmi (op. cit.) says that the "Amen" should be stretched out to the time that it takes to say: "Kel Melech Ne'eman". I think that many Ba'alei Koreh pronounce their "Amen" in roughly that amount of time.
See the Mishnah Berurah on this: MB OC 141:17.