@wolfmanbush
If the vision / intent of the game environment is to emulate pirate era fantasy seafaring then by all means coordinated fleets belonging to the same group would be part of that environment. Take the most famous example, Pirates of the Caribbean (literally also in this game). There are armadas in the series that the main characters must interact with, form alliances against, and defend themselves from. Creating fleets has been a mechanic since year 1, but only for Alliances between online strangers.
I think your belief that game activity should be 'random' doesn't make a whole lot of sense either, otherwise Alliances and Commendations related to inter-crew cooperation wouldn't be part of the game as they require coordinated effort between multiple crews.
'Organic' or 'contrived' gameplay is a completely subjective criteria unique to each individual player, as well as 'strong' or 'weak' alliances. What is an objective fact is that for 4 years players have been asking for the ability to play with more than 3 additional friends while adventuring.
The bottom line is that as long as Alliances are a mechanic within the game, there's no reason they can't include Alliances between existing friendships. It doesn't make sense to exclude a feature if the exclusion of that feature actively drives players away from the game. Ultimately the goal of any video game is player engagement.
If Rare's worry is that PvP will become unbalanced, then they should at least offer the ability to have a closed server (god knows there are plenty of empty servers) or a PvE mode (another request by players for multiple years). By not offering some compromise like this, Rare is implying (whether intentionally or not) that large groups of friends are not welcome.