Alpha is not a reason to break every single existing ship for zero reason. What does block-based directional thrust actually add to the game, besides making building a ship a bigger pain in the ass, and, as stated previously, requiring you to make a shitty ball of thrusters instead of a 3 block long stick when you just want to be able to quickly move your ass from point A to point B around a sector?
Relax, my idea isn't new or obscure, it's obvious. The devs have undoubtedly considered it in the past and decided not to use it.
It's just that the OP's idea adds nothing to the game. It's effectively identical to the system we have, except that your thrust profile may change as you take damage. So he may as well either not make the suggestion, or go all the way and suggest thrust by module direction.
But just for the sake of it, to reply to your actual post:
It would be trivial for the devs to include a conversion to the new system which would just rotate existing thrust blocks according to the percentages in the thrust settings. No need for anything to break. Did you object to the removal of docked thrusters breaking ships? There's no auto-conversion for that.
What it adds to the game is more control than the current system: forward, back, left right, up down all become individual values, so there's more scope for lowering thrust in chosen directions to improve ship efficiency.
Also it would allow "swing-wing" designs, where docked thrusters can be rotated to change the thrust profile on the fly as needed. All manoeuvrability thrust could be diverted to forward thrust to escape a fight for example.
It would also allow for tugs to move large ships into docks faster than they can move themselves.
The terrible, terrible cost and inconvenience of placing 5 extra thrusters requires a pretty dramatic point of view to describe it as "shitty" compared to one with 5 less thrusters. I doubt it would factor into the decision of any new feature.