It may be a handy mnemonic, but it's not the etymology (you may know this, but I can't resist the pedantic opportunity!)

It comes from Swift's satire about egg eaters. The end in question was the small or large end of the egg and Big Endians broke the big end with the spoon - i.e. it went into the egg cup small end down.

The -ian suffix here is analogous to Christ-ian or Keynes-ian and has nothing to do with "in".