Maria always cared for Shadow and risked her life to save his while Elise is just someone in someplace who can't cry or the world will end, which it has. Also, all you had to do was kill Elise and Iblis would be free because the host is dead. Mephilis wouldn't have to go though all that trouble into killing Sonic. I don't know which is scarier:
Weirdly, when I first saw this scene, I didn't think much of the kiss other than "gee, that was poorly animated" and cheesy as all heck. It wasn't until well after the fact that it occurred to me just how...bizarre...it actually was.
The cast reactions is just perfect. All across the board.