How to fix/clean burnt MagSafe 2 connection
Yes, those are definitely burnt and this is because the sand allowed a gap just large enough that the electrical current arced from the adapter to DC-In port.

You can't clean this with alcohol - that's actually the last step.  What you need is something that's mildly abrasive.  You may have more luck cleaning the MagSafe adapter because those are pins where as the DC-In board are four conductive "dimples" surrounded by the most fragile plastic you'll ever run across.

What you can try:


Solder Wick.  Take a small piece and using a blunt tool (pen, pencil, etc.) and work it back and forth like a Brillo pad.
A very tiny piece of 800 grit sand paper (tiny enough to fit inside the DC-In port indentation) and work the same was as described with the solder wick.
Make a slightly moist paste of Bar Keepers Friend and water and "scrub" with a cotton swab (when I say slightly I mean just shy of being dry).  


Once you've "scrubbed" the contacts, you can then use the alcohol to clean the contacts properly.  Basically, it's like cleaning "burnt on" anything  in the kitchen - you've got to scrub it off first, before you polish it.  Until you get it clean, it's not going to make proper contact.

If all else fails, the DC-In board is actually very cheap and very easy to replace.