I suppose sunscreen would help, depending on your skin sensitivity, and how exposed to the sun you are, but quite frankly it seems silly to take a drug that's known to increase sun sensitivity when you know you're going to the equator and are going to be on the water for an extended period of time. Most divers take Malarone because they have acceptable results while using it on dive trips.
If it were me, unless the doctor could cite lots of literature supportive of Doxy and against Malarone, I'd get a new doctor.
Btw, I've never had a doctor who was adverse to prescribing Malarone.
I'm sure you'll have a great time whichever way you go!