A very different perspective on Shechita - Helping souls achieve their tikun

I was always under the impression that shochtim saw themselves as people providing a valuable service to the Jewish people by providing kosher meat. However, Mishpacha (Hebrew) had an interesting article last week about the Kosher meat industry in Argentina. As part of the article they interviewed Rav Asor who is the head shochet (as well as the oldest and most experienced) for both the Rabbanut and Badatz Beis Yosef in Argentina, and he provided a very different perspective as to how he perceives himself.

"Do you think I look at the animals with the eyes of a butcher? No, I look and think about the many souls that are gilgulim in these animals that are waiting for a tikun, and how much these souls will be helped when the meat that are in will be eaten at the seudas mitzva of Pesach night. I truly feel a shlichus.
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I don't just think I know. Sometimes I see the tears in teh eyses of the animal, and I had some cases where the animal itself stuck out ist neck to my knife. At the last second you can see that the soul inside wants to get out. 

The truth is that there is no source for gilgulim in the Gemara, in fact, there is an explicit Gemara that seems to contradict the whole idea of gilgulim. The Gemara in Bava Metziah (107a) comments on the pasuk ברוך אתה בבואך ברוך אתה בצאתך that it is teaching us that just like a person enters the world without sin he should leave the world without sin. The רש"ש there comments that this contradicts gilgulim. The reason being, that the premise of a gilgul is that a nefesh that already sinned comes into the world to be מתקן that sin. However, the gemara states explicitly that a person comes into the world without sin. Gilgulim is a Kabbalistic concept which was popularized by the Ari and has now become part and parcel of Charedi Judaism.

If you are a rationalist does this statement of the shochet bother you? Does this make you have any doubt about the shechita?