Yes that's true. I might do like I said before and add another stat, like: Ruby +1 Attack / +1 Fire resistance.
But that would tie some stats to some resistances

Or I could have each item have two slots, one for stats and another for resistances, and each gem would give a different bonus depending where you put it. Could increase the other gems to have even higher stats.
Like:
Amber Pebble
on stats socket = +1 attack
on resistance socket = +1 fire resistance
Ruby Pebble
on stats socket = +4 attack
on resistance socket = +4 fire resistance
so Ruby would be a sort of "upgrade" to Amber, and of course more valuable. I think that might be the best solution... will need of course to test and tweak so that players don't become too powerful (but would be enough to raise the cost of gems probably!)