The immobilizer system on these bikes can be VERY EASILY disabled via the ECU. So no, its absolutely not a deal breaker what so ever. If you want another key made, simply do a google search for "immobilizer disable Ducati" and you'll see the companies who do the software update. Then you can have a standard key made, instead of a special one with the electronic ID built into it.
The key card is necessary for reprogramming an ECU OR ordering a new key from Ducati. I've never quite understood the reason for the red key however. My new 848 didn't come with one, just two black keys and a key card. So they clearly ditched the idea after the 749/999.