Another idea would be to treat Giant Sizing as a special rune itself, in that you have to sacrifice one of your active rune use to trigger it, so you'd only see two effect per short rest no matter what. And if you rule that two such effect can't be active at the same time, then you'll probably only see 1 Active per fight since the fight will probably end before they can trigger another one.That's a good idea. Hmm... I need to think about which would work best.
If you think it's still too strong, make the Giant Sizing ALSO deactivate the passive ability until they can engrave the rune again next long rest. I'm personally a fan of sacrificing long lasting passive bonuses for a powerful short time effect.
Personally I always felt the giant sizing thing detracted from the cool rune concept more than anything I would have preferred more runes at third level and giant sizing be made stronger as a capstone ability instead.