It is not an evil act, but it isn't good either
The ability doesn't mention anything about it being an evil act, only that it is a death effect, and those are allowed normally on PFS games. Also keep in mind that casting [evil] spells are not automatically evil acts on PFS either but that depends on how the spell is being used, as explained by James Jacobs. Though the final decision is up to your GM, he is advised to warn you that you just did an evil act and that there will be consequences if you keep that up (according to the manual, page 14).
The ability is no different from a magical coup-de-grace and that action isn't considered an evil act either. The ability also doesn't described that you actually consume the soul, despite the ability's name, which was confirme by a developer:
In fact, the idea is that you watch it go about its normal way and study the results. Macabre, but a step up from daemonic soul-sipping. You're basically killing it in a controlled environment. Y'know, for science.
Yeah, still really not a Good thing to do.
If used to finish off an enemy and activate your abilities, that's fine, it's a morally grey act, but if used to kill an innocent just so you can activate your abilities, the GM should warn you at first, then apply an alignment shift towards evil if necessary. Keep in mind that a character who becomes of evil alignment will be marked as "dead" on the chronicle sheet.