I mean, you could make it trash as many cards as you want at once, in which case Fortress doesn't break it.
You could also make it impossible (or very difficult) to have more than one in your deck, because then having both it and a Fortress in your starting hand is difficult, and doing it reliably would need a third card, and three card combos can be as nuts as you want. Prizes, one-shots with weird buy/gain requirements, maybe as an event...
Or you could make it set aside the cards, and then do whatever with them during cleanup (trash them, put them on top of your deck, etc).
Just because its interaction with Fortress is too powerful doesn't mean that you should drop the idea altogether.