The way to make sure that you get on a cheap flight from South Africa to Maputo is by:
typing your flight details into the flight price comparison tool and see what airfare it spits out
check the airfare of every airline flying from Cape Town/Johannesburg to Maputo (listed on the link below)
There is no time difference between Mozambique and South Africa.
Don't expect flawless infrastructure, rather think of Mozambique bas being a porch overlooking the Indian Ocean, and Maputo its entrance. The beaches in Maputo aren't great, but a quick island hop on a charter flight to Inhaca will give you all the beach you desire (and while you're there take a trip up to the top of the lighthouse to enjoy the view).
If you're into the macabre pop into the Museum of Natural History to see the world's only collection of elephant fetuses.