"Over zealous agent"?? Hardly! They can't possibly know all the visa requirements for hundreds of countries. Delta's programming alerted the agent at check-in to verify a Schengen Visa because of the length of time it "assumed" he would be in the Schengen zone. As mentioned by others here, the Passport stamps will be the proof he needs if questioned down the road. A hotel receipt from Croatia adds further evidence of his length of stay outside of the Schengen zone. Chances are slim or none that he will have any issues getting to Venice now that they let him on the first flight.
All airlines are very touchy about letting people on an international flight because they face large fines if a passenger arrives somewhere and is not admitted due to lack of a valid Passport or visa. In Venice, they will ask your son how long he is staying in Italy and the answer is only a few hours. That should suffice, but a written copy of his full itinerary and confirmed hotel reservations will get him through with no issues at all.