I would probably do, basically, what Wolf suggested and replace the Thief with one from a later game, but probably not from 3 due to the whole not needing keys to open locked doors thing, though I'd also replace the Ninja job with the FF6 version instead of leaving it as it is. There's no value to the black magic the class gains in FF1 outside of haste, so giving the players elemental damage via scrolls instead seems like a fair deal.