I think the sales are so bad, where as they might usually go into working on a sequel, this may have jeopardised the entire franchise. Reviews don't pay for a sequel to be funded, sales do and at the moment sales are poor and potential future sales have also been jeopardised.
They may have been a great plan of going up against Uncharted and creating a big buzz in addition on piggy backing on Uncharteds hype, but that didn't happen. They put all their eggs in one basket and royally got their asses handed to them.
The game has been given away for free in bundles and been discounted within a few weeks of launch and it still failed to do good in sales. For a big franchise, that's really concerning.
I know there are hopes of making money back on the PC and PS4, but if you look at the games being released in 2016, they are in for a tough fight. I don't know of a single PC or PS4 gamer that is willing to pay full price on a 6-12 month old game.
As for what money MS gave, I don't think they covered the bulk of development costs or even half. If they did, SE wouldn't have done the panic release of a statement they did giving away the release dates on other platforms