The Cougar Point chipset, which will be used for Sandy Bridge MacBook Pros, has two SATA 3 ports on it. Which also happen to be the two ports that don't have problems.
So yes, Apple will use them.
And yes, you will be able to replace your standard HDD with a SATA 3 SSD. Although I expect Apple won't sell them BTO, so you will likely have to do it yourself. But that's OK, you'll save yourself a lot of money.