Not to be insulting but if I were your brothers kids I would not be concerned about you disowning them because they should be the one disowning you... Instead of holding out an olive branch with some hope that they may one day gain interest in their Jewish roots you do the very thing that might push them away forever... It's not their fault that their father decided to marry a Gentile... Hopefully you have some other grievances to go along with the fact that they were born of mix faith relationship... Honestly I believe you might have lost an opportunity to make a big difference in their lives after your brothers passing.
Honestly this is a struggle I deal with every day. The primary issue was that my brother and I, while close in our youths, had issues when we were grown. My brother was always the 'good guy' and I was the older brother who would get into trouble. My brothers 'goody-two-shoes' image really bothered me, and in some ways it bothers me to this day.
I suppose I could reach out and show them the reason it is important to maintain Jewish identity. But inside me there is also jealousy for my brother, his success (which eclipses any success I may have made) and his wealth, and his large number of friends (I have been mostly a loner/geek). He had two children, while I have none (due to my own problems in my previous marriage)...
Anyway, I hope that this will be resolved some day... I really feel bad now because I embrace my Jewish identity, am proud of it, and yet I don't have any children to pass this on to. This is one reason I try to teach others about Judaism because the sages have said that a teacher is like a parent, in that the good things he teaches will grow into future generations..