Spoiler Level: High
Aww, man. I guess all Silurian stories have to have unhappy endings.
Geez. Not only did Rory not break through the "second companion can only be here for three stories" glass ceiling, he got the harshest exit of any companion since Sara Kingdom. On second thought, his was even worse. Sara may have got aged to death, but poor Rory gets erased from history so even his own fiancée doesn't even remember he existed.
And it's a real shame, because I really liked the interplay between Rory, Amy and the Doctor. Having two companions that were an actual couple was totally new for Doctor Who, and I think they really missed an opportunity by getting rid of him.
I suppose there's a chance The Crack might bring him back or something like that at the end of the season to give him & Amy a happy ending, but we'll still be without him in the TARDIS for the rest of the season. And I have to assume he won't be coming back, and that this is really it for him.
I'm guessing the military class Silurians used the masks for the same reason the Judoon and Sontarans use helmets-- this way they only have to do face make-up for the main characters. But I think the masked Silurians looked much cooler.
I also liked the idea that humanity and the Silurians were actually reaching an accord, and that they finally will in the future. In addition to giving the story a silver lining, it creates some good opportunities for potentially using them again.