Maybe get in the queue for non EU citizens (assuming they have separate channels there)
They do have separate channels, but the maltese can be sticklers for correctness and may decline to stamp the passport.
On the other hand, most are also quite kind and love kids, so I guess it just depends who you get on the day.
Enjoy the islands - its very hot at the moment (30s) and pack plent of high factor suncream, as the sun is merciless at this time of year.