A few things:
1) Passing such rules as leave the village/ break the marriage etc are not ever going to solve this problem and will just end up ruining/ending some lives which is by no means something that can be ignored.
2) The problem of same village marriages is not going to be a big happening/problem anytime soon. And it can be limited very easily by just making the kids aware of the culture. Although one can not very logically say why shouldn't such marriages be allowed because in big enough villages, many families are not connected for several generations back. But still people may choose to agree to some kind of customs and sometimes may not, which doesn't seem very probable atleast rightnow.
3) Not allowing marriages in a different village which has same gotra is something which we really should now give up for the sake of betterment of society as there is no way of logically defending it and it is not doing any good to anyone and there is no reason for any fear as there are societies which don't have such rules and are happy, prosperous, civilized, educated without suffering any harms. There have been many instances in history when several of cusoms and beliefs had to be changed according to the need of time and logic (for example purda which is again a custom doing no good to anyone (quite a lot of harm though) and cannot be continued just for the sake of customs).
4) Regarding love marriages, which people think should be broken because of the gotra problems..
Love marriages are not at all easy to make and it is generally very very difficult to find someone whom you feel you love and can take a decision to spend whole life togther. There are so many people who would like find that person but their surroundings won't have such people. And those lucky ones who are able to find one, please let them live happily. They won't get that chance again. Otherwise why would people want to stick to the people they love despite so much harassment coming from all sides.