It seems that you have some misunderstanding. Abdul Nasser Madani was acquitted for want of any evidence against him. And the person who helped him was none other than Retired Supreme Court Judge and Human Rights Activist, Shri. V.R. Krishna Iyer. Not even the Muslim League had helpped him.
Have you heard the speaches of Mr. Madani after his release from the jail? He does not talk about Islam or the need to make the whole of Kerala an Islamic Caliphate, etc!
Of course the composite culture of Kerala is under attack from the religious fundamentalists of all hues and that needs to be resisted at any cost.
The Govt of Kerala should do something like what they did to the Naxalite movement in the 1970s. Bitter pill for incurable ailments!!!!!