John Stott has some wise and measured words on this subject.  He is, of course, writing from within an Anglican context.  But I think that the principles he espouses are worth weighing in other parts of the church too.

What should the contemporary church do with heretics? Is that a harsh word? I think not. A humble and reverent probing into the mystery of the incarnation is the essence of true christological scholarship. But attempted reconstructions that effectively destroy that which is supposed to be being reconstructed is christological heresy.Let me defend my question further. It is based on three convictions: there is such a thing as heresy, that is a deviation from fundamental, revealed truth; heresy ‘troubles’ the church, while truth edifies it, and therefore if we love the truth and the church we cannot fold our arms and do nothing.

The purity of the church (ethical and doctrinal) is as much a proper Christian quest as its unity. Indeed we should be seeking its unity and purity simultaneously.

I do not myself think a heresy trial is the right way to approach this. Heretics are slippery creatures. They tend to use orthodox language to clothe their heterodox views. Besides, in our age of easy tolerance, the arraigned heretic becomes in the public mind first the innocent victim of bigoted persecutors, then a martyr, and then a hero or saint. But there are other ways to proceed. The New Testament authors are concerned not so much about false brethren as about false teachers…Is it too much to hope and pray that some bishop sometime will have the courage to withdraw his license from a presbyter who denies the incarnation? This would not be an infringement of civil or academic liverty. A man may believe, say, and write what he pleases in the country and the university. But in the church it is reasonable and right to expect all accredited teachers to teach the faith that the church in its official formularies confesses and that (incidentally) they have themselves promised to uphold.

Stott, Authentic Christianity, 121.