Those who won't accept sagotri Hindu will not accept the guy from another religion for sure, but you can try being a Mussalman. It allows you to have four wives anyway.

Seriously, I think it is a big problem for you. It is almost like marrying in your own family. Several years ago, when people entered Nepal, moved from one place to another, they were allowed to change their sirname. But to avoid incestual marriage, they kept track of their Gotra. I have heard that Acharyas who went to Kaski from Jumla were called Parajuli, and so on. So you can see what it means.[ Of course, this is true in India too]

Funny thing is I have seen several intercaste marriage, but  sagotri marriage is hard to find. It is like marrying in your own family, and people feel extremely uncomfortable about it. It is almost impossible to find . say, Khanal marrying Khanal or Aryal marrying Paudel. So if you marry let me know so that I can remember you as an exception.

Finally, do whatever pleases you. Afterall, several people marry within their clan too. It is just that we feel very uncomfortable about it.