MacBook Pro 13" Unibody Mid 2009 Teardown
I don't really get the issue with the SD card sticking out -- seems like a normal design to me. You want to be able to have enough sticking out to grab onto to pull it out! If you had a flush mount you would need some sort of spring mechanism with a catch (like my digicam internals) or a spring and release button (kind of like the old pcmcia card slots). More mechanics/moving parts == more things that can break down IMHO.
Even my plugin USB SD card reader has this exact same clearance and I've never had an issue with it. Not like you would (should) be porting around your mac in your laptop case while you had an SD card plugged in. (although I know people who leave CD's in all the time but I think that's kind of dumb too.)