So why are Sion and Swain rivals again?

Sion is generally out of his mind while out of combat....and during that time see's Swain as Boram Darkwill, the Grand General that he remembers.

Its only while in the thick of combat that Sion starts to see clearly and see's that Swain is not his General, but those moments are fleeting and once the rush of battle dies down he again loses his grip on things.

I guess Sion disagrees to be someone's tool or something, but that's just a random thought.

Sion is Swain's rival because Swain represents everything Sion detests in Noxus; underhanded, scheming, manipulation. Sion loves and remembers a Noxus built on the merits of true strength, which is everything Noxus currently is not. In a similar vein, that is why Riven went into exile after seeing that contemporary Noxus had no qualms about employing efficient, but inhumane battlefield tactics, let alone betraying their own forces.

Most of the time sion simply sees swain as his leader,he sees him as a strong leader who doesn't back down no matter what.

However sion was warned to "beware of the ravens" and hates what he has become,there are times when sions mind becomes a bit clearer and he realizes this. Swain is using underhanded tactics,which probably goes against Sions principles,but sion can't break free from swains control.