The col is under arrest in the Malegaon blast case … he is not part of the Samjauta Express blast. Just an update .
As regard the hindu terroists or any terrorist … action is taken against them irrespective of their religious affiliation. You see we dont have an “army of God” to protect 
In any case India has had a good record of handling sepratist or terror organisations … but there are countries in the region who have failed to do so and are suffering due to this.