You're entitled to your opinion. Software developers make decisions for various reasons, generally knowing they aren't going to be able to please everyone.
I agree with deleting a file. If I delete it, I want it to go away. But the file disappearing beneath the application without user intervention in the application is beyond the application's control. It seems logical and reasonable (to me anyway) that the only thing the application can do is keep the contents of the buffer. I would be pretty hacked off if the application made a decision such as "Well, the underlying file is no longer there. I don't know why, and I don't really care. Let's just trash the buffer as well." That is not what I want an editor to do.
This is not the appropriate forum for discussing how SCMs work.
Again, if the user initiated the action through ST2 that caused the underlying file to disappear, I would agree that closing the buffer is a good idea. But if something happens outside the control of ST2, I don't want my buffers suddenly disappearing. Don't forget that you can put your idea up for vote over at UserEcho  and if enough people agree with you, it will bubble to the top and get Jon's attention.