It would depend under which act is the association registered. Is it the co-operative societies act or the apartment ownership act. The provisions of such act would have to be read with the terms of the sale deed and anything contrary to the act, would negate the terms of the sale deed and could invite litigation.
If the terrace area is not a common terrace and has no entrance except from within the flat, then the society will not be entitled to put up any tower on the terrace area. You can file a suit against the society for restraining them from tresspassing into your property and also for removal of the tower.