We just got back from Azamara cruise with Maputo stop.
YES, they arranged for the visa. $50 pp. They gather the passports of those that want to get off the ship and when you get it back, it's got this lovely Visa stamp in it. You don't even get your passport back to disembark the ship when you get to Maputo. That's done with your cabin key card. So, it's easy as can be, no worries.
We ended up doing a FREE walking tour, which you can easily find & book online. Totally worth it. If fact, the same guy through whom we arranged the tour handed us off to a colleague and guided the ship excursion tour. Same tour, his was shorter and more expensive.
It's a nice walking tour which I highly recommend. Fort, train station, plazas, several parks, and you do learn a lot of history. We did miss the beach, so if you want the beaches, which I hear are beautiful, this is not the tour you want.