My guess is that power entered the three-switch box and then was split to feed all three switches (two of which were used for the old fixture). You shut off the two switches to the old light, replaced the kitchen fixture with one only requiring one line, and then only reattached the power from one of the switches.
Leaving the unused line where it is is fine. I would cap it off in the ceiling fixture box and I would definitely remove the power to the unused switch and remove the old line from the unused switch (capping it off in the switch box). Probably the best thing to do at that point would be to remove the unused switch from the box and put a cover plate on it that only accommodates the two switches in use. Not sure if they make those, however.