I agree with your overall assesment, the young Xanthe wont kill and has no interrest in killing the twins, it would just be stupid.She'll be fine not because of any weird shopkeep shenanigans (I doubt the twins could "offer" him anything that would be worth being an "enemy" of the MC), or because of any meta "muh waifu hasnt had a fight scene yet" reasons, but because Yung Xanthe isnt a dumbass and he clearly knows what he is doing. He is obviously doing more than necessary (for a normal monsterfication) but the idea that he is going to kill her is almost laughable.
1. they (sin) just wasted time, resources, and an extremely powerful and intelligent monster to "get" the twins....as well as whatever was needed to summon the monsters/any other preparation all for xanthe to just bisect her and kill her? While she wasnt even able to feel most of it? Even if Xanthe was the "head" of sin and that was the goal all that would do is make sin look like a joke instead of a group that is "close-ish" to hero
2. Ella (and likely sins) plans clearly require MC not stopping them or even being on their side..... and directly after kidnapping MC yung xanthe decides to kill one of his harem/oldest friend? Unless he plans to build a full ass robot (that mc cant tell is a robot) killing her would serve only to ensure that MC will not side with SIN since we know as of the bonfire that MC values the "cast" as either the most important or the only important people to him
But about your 2) i dont think anyone but ella views/considers the mc important for anything, i doubt ella shared her true goals with sin, it seemed more like a relationship because some of their goals (ella&sin) were the same but not even close all of them. Or is Xanthe the one who guided Ella on this path? It could be but i dont think so.
But yeah i dont think SIN really gives a fuck about the mc or the way he reacts to stuff they are doing. He's just a level 3 who somehow ended up as the mascot from hero (which may makes him a bit more valueable).