Although you would be arriving from outside the Schengen area, you are still travelling within the EU, and therefore it is unlikely that the Maltese immigration officers would spontaneously stamp your passports. However, you could ask them (nicely!
) if they would give you a stamp.
I'm a UK immigration officer, and get asked a lot if I would stamp EU passports. The only trouble with that is that we would then be imposing landing conditions (such as no working or claiming state benefits) that as an EU citizen you are entitled to!
The other thing I would add is, don't write in his passport as a record of the trip.
Many countries take a dim view of non official endorsements in passports. Also, you run the risk of filling it up like this, and if there is no room for a stamp or a visa, some countries will refuse entry.