According to Wikipedia, A Hostage With No Compromises was not aired "because the plot involved child kidnapping and in Japan, real-life child kidnappings were making headlines at that time", and as mentioned in the question, A Fruitless Lunchtime and The Man From the South was aired as episode 1 on August 26th, 2003.
The Japanese article of Full Metal Panic! reports that Fuji TV made the change to the airing due to the kidnapping and murder case in Nagasaki that happens less than 2 months before the airing date.
Below is the summary of the incident, based on the ariticle:
On July 1st, 2003, in Nagasaki, a 4-year-old boy was kidnapped and murdered by a first year middle schooler (12-year-old). The child was led by the middle schooler to the top floor of a parking building, where the child was stripped naked, then was punched and kicked in stomach and various places. Furthermore, the child has his genitalia mutilated by the middle schooler with scissors. However, when he realized that there was security camera, he decided to throw the crying child over the railing down the road 20 meters below, the impact of which killed the child 30 minutes later.
Looking at the summary of A Hostage With No Compromises (taken from Wikipedia):
After Sousuke's encounter with a gang leaves its members disrespected, their leader decides to take Kaname hostage. Instead of giving in to their demands, Sousuke holds the gang leader's little brother hostage and proposes an exchange.
The story was quite similar to the outrageous incident, not just the kidnapping part, but also the part about a young man kidnapping a boy.