I have read many reports that Gaggias with their aluminium boilers do corrode. And one retailer has abandoned them for that reason.
Perhaps you should remove the boiler again, dismantle the element, then scrub the boiler, and soak it and the element in a bath of citric acid until they gleam.
If the pitting is very deep, i.e., almost through the wall, will the boiler safely hold steam under pressure? Worth considering.