Hi Scott,
You won't need a yellow fever vaccination coming in from La Réunion and/or Mauritius. You would need to have been to a yellow fever area on the African mainland.
On flights: you would have to change planes in Jo'burg to get to Cape Town - there are no direct flights, but as you say, that shouldn't be a problem.
The only airlines operating regional flights out of La Réunion are Air Austral, Air Madagascar and Air Mauritius, so it's a sellers' market. Long haul operaters like, for example, Corsair, aren't allowed to pick people up in Réunion for the hop to Madagascar. You could try talking to one of Air Mad's call centres - they will usually give you a better price than anything quoted on their defective online booking system. If you're in the UK, the Paris Centre (0033 892 70 18 19) is your best bet. They'll give you any discount that's available and also arrange for your tickets to be held for picking up at Réunion or Mauritius if you want.
Camping is allowed in many of the National Parks, especially those where trekking is part of the visit, and is safe there. Whether or not it's officially allowed outside the parks I don't know, but if you want to try it, you should make contact with the headman of whatever village you're near and ask his permission. If he grants it, you would normally be safe. In point of fact, though, apart from on treks camping isn't really necessary, as even in quite small settlements there is often a "hotely" with basic facilities for very little money.
When I spoke of "centres", I meant the important towns themselves. There are no "guide centres" of the kind you mean apart from those directly attached to the National Parks, but that's not the sort of guide you're looking for here. Talking to the owner of your hotel is your best bet for both guides and vehicle hire.
I wouldn't like to quote you a price for a hired vehicle from Tana down to the south or west, as the last few times I've used the local ground transport ("taxi brousse") and prices are rising rapidly anyway. Petrol now costs around 1.20 euros a litre, which is almost a European price, and that is really pushing up the cost of travel, especially as poorly maintained vehicles use more fuel. You might like to take a taxi brousse down to Antsirabe and make enquiries about contacts at the Arche restaurant/café or at the operator opposite the Arche (whose name I've forgotten). You'll probably get a cheaper deal than in Tana, and Antsirabe is a pleasant place for a stopover. Whatever you decide to do, keep in mind that if you hire a vehicle and don't make a round trip back to your starting point, you will have to pay for the cost of the fuel (high) and driver (low) back to the starting point.
Rakotoson is at least honest in that he doesn't try to conceal that he is an operator/guide. What he unfortunately does conceal is how to make contact with him! What he's offering is a standard trip to the standard attractions along the tarmac road from Tana to Toliara. Nothing at all wrong with that - they're all worth seeing and it would make a rewarding experience. But if you want to get more off the beaten track and visit less frequented parks such as Andohahela or Tsimanampetsotsa and see some of the remote scenery around the south and south-west, then you would need to get down to Fort Dauphin/Tolagnaro or Toliara and hire a 4x4.
If you do decide to go with Rakotoson or a similar operator, you may find that the first price quoted is for a group trip on which you'll find yourself together with a random selection of other foreigners who you may or may not get on with. Such tours, for obvious reasons, allow very little flexibilty. If you ask for a vehicle just for yourselves, you'll pay more, but you'll have the flexibility to stop where you want, change the route spontaneously or whatever.
Enjoy.
