It is a game, and if part of the long term goal is to introduce "guilds/clans", then TS is and will remain a necessary element of skilled teams.
There is a reason in WoT that TS3 is essentially required by all top clans. Players that intend to work as a team will move towards a system that increases co-operation. Nothing funnier then seeing people in the CW channel asking if ingame chat would work because none of their guys were on TS.
Also, think about how long it would take to send and receive messages via signals flags. "range shot, range shot, broadside, trim sails, crap gotta decode, full sails, coming about, range, range, crap have to send a return message, range range, broadside, what was message again?!?!"
Finally, I don't think that there is anyways to stop people from using TS. End of the day, its a game, not an absolute simulator.