First of all it isn't that simple. Do you know the shit storm that would arise from DQ'ing someone like REO, Jr, 16bit, etc? Almost EVERYONE who travels for MK9 is a killer, so DQ'ing anyone will really shine a negative light on whoever makes that decision. Regardless of why they were DQ'd. People would be screaming "Illuminati" from the roof tops. And would you really DQ someone that has traveled all the way to Philly from the WC just because they aren't present on time? Legitimate problems arise, people aren't always late just because they're lazy.
Second of all, have you ever ran a tournament? Unless you have the money, time, and man power MLG has, it isn't so black and white easy to handle. It takes hard work and dedication to run a tournament, I'm sure most people have seen that first hand. And as far as I know, they're not getting paid to run the MK tournaments, they're doing it for the community.