you'd absolutely have to make sure it was a defined pattern that was balanced well to the size and shape of the room. The idea would be to make the inlay look like an original design feature.
Obviously, this might mean cutting out a much larger area than the stain, or cutting several similarly sized areas throughout the rug.
I think this would work best in a dining room, and least in a living room because of the furniture layouts. Depending on potential buyers, it might lower resale value if you were planning on selling soon, but IMHO, not as much as an obvious patch would.