Here's an idea:
Since it seems to be very difficult to actually break up a set of irons. Why don't we get one or two more slots available in our bag. Then, if we choose to add a single club (like a 4th wedge or a hybrid) we have the option to "disable" or make "unavailable" a specific iron in our set. This way, the sets don't get broken up and we can still use our individual clubs as we'd like.
Not really any different than in real life finding you had an extra putter in your bag when you left the practice green and went to the first tee in a tournament and instead of tossing one to a person in the gallery, you simply declare it as ineligible for use during the round and it rides happily in the bag until you can finish the round... and fire your caddy.
Allen