What you're describing was actually implemented towards the end of version 1.0 - it was called 'Caravan Security' and was a requirement for creating relic weapons. Presumably SE decided it was too complex or difficult though and instead cut it down to the basic 'escort FATEs' we now have in ARR.

If you're after Allied Seals, just do the daily and weekly Hunts, you'll soon gain a fair few seals.