A lot of people can give an apt reply. Let me also try it.
First of all let me clarify, numeral times khaps have passed positive verdicts on the present devil issues in society. you can see some of the verdicts here..In these cases khaps intervened in some family rivalry, passed resolution against female foeticide, dowry etc..but till data media did not pay heed to cover this positive side of khaps..and khaps were always presented in bad taste
http://www.jatland.com/forums/showthread.php?30884-Collection-Khap-s-Positive-Social-Verdicts
Now if we come to your question. May be it looks a bit harsh to you. Same gotra marriage is a *SIN* in Jat society and that is not acceptable anyhow. I don't find anything wrong in ostracizing the families who are not in accord because if such steps are not taken, more people will follow the same path..that in turn will destruct the foundation of Jat society. As far as killing is concerned, that is not justifiable at all.