There's a scholarly article on the Inquisitions at a [rather surprising website](http://www.ironmaidencommentary.com/?url=album10_xfactor/inquisition&lang=eng&link=albums#theological). It says...

> (From Deuteronomy 13 NIV) "If a prophet, or one who foretells by dreams, appears among you... and he says, 'Let us follow other gods'... **That prophet or dreamer must be put to death... You must purge the evil from among you.**
>
> If your very own brother, or your son or daughter, or the wife you love, or your closest friend secretly entices you, saying, 'Let us go and worship other gods'... do not yield to him or listen to him. Show him no pity. Do not spare him or shield him... **You must certainly put him to death. Your hand must be the first in putting him to death, and then the hands of all the people. Stone him to death...** Then all Israel will hear and be afraid, and no one among you will do such an evil thing again.
>
> If you hear it said about one of the towns the LORD your God is giving you to live in that wicked men have arisen among you and have led the people of their town astray... then **you must inquire, probe and investigate it thoroughly.** And if it is true and it has been proved that this detestable thing has been done among you, **you must certainly put to the sword all who live in that town. Destroy it completely, both its people and its livestock.**
>
> Gather all the plunder of the town into the middle of the public square and completely burn the town and all its plunder as a whole burnt offering to the LORD your God. It is to remain a ruin forever, never to be rebuilt."
>
> (From Exodus 22:18 NIV) **"Do not allow a sorceress to live."**

It does appear that the only NT verse which could be used as justification is the one you cite from John 15. However, S Thomas Aquinas was happy with the situation of heretics being delivered for execution:

> ...Wherefore if forgers of money and other evil-doers are forthwith condemned to death by the secular authority, much more reason is there for heretics, as soon as they are convicted of heresy, to be not only excommunicated but even put to death.
>
> On the part of the Church, however, there is mercy which looks to the conversion of the wanderer, wherefore she condemns not at once, but 'after the first and second admonition,' as the Apostle directs: after that, if he is yet stubborn, the Church no longer hoping for his conversion, looks to the salvation of others, by excommunicating him and separating him from the Church, and furthermore delivers him to the secular tribunal to be exterminated thereby from the world by death... Arius was but one spark in Alexandria, but as that spark was not at once put out, the whole earth was laid waste by its flame.
>
> [*Summa Theologica*]

As to whether the Church should be acting in the same way today, what Aquinas says is relevant: "...and furthermore delivers him to the secular tribunal to be exterminated..."

Aquinas acknowledges that it is not the Church who is exterminating, but "the secular tribunal". People are put to death in accordance with the laws of the State, which may or may not allow execution for heresy against the Church. Most secular law nowadays does not.

With excommunication, the Church is protecting itself from pollution — both the Church Militant as the heretic will no longer have contact with it; and the Church Triumphant, as he won't reach heaven either.

The Church [does still excommunicate](http://www.lifesitenews.com/news/brazilian-priest-excommunicated-for-heresy-for-denying-catholic-teaching-on/) for heresy.