Sanctifier En-Vec's last ability cares only what the color of the card would be in the zone it's moving from, not what it would be in the graveyard. For example, if a Clone is a copy of a red creature on the battlefield and then dies, the Clone will be exiled. Conversely, if you cast Order, the white half of the split card Order//Chaos, it will not be exiled as it resolves because it is not red before it goes to the graveyard.
If a black or red permanent would go to the graveyard at the same time as Sanctifier en-Vec, that permanent will be exiled instead.
If a black or red spell causes Sanctifier en-Vec to have lethal damage marked on it or causes it to have 0 toughness, Sanctifier en-Vec will not be put into a graveyard until the next time state-based actions are checked after the spell has finished resolving. In this case, the spell will be exiled instead of going to its owner's graveyard.
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If a black or red spell causes Sanctifier en-Vec to leave the battlefield as part of its resolution, that spell will go to its owner's graveyard and won't be exiled instead.