firstly, i’m so sorry that those things were said about your baby boy, that’s so hurtful and rude.
if you have your heart set on rueben, i’d say go with that. it’s such a lovely name! i personally wouldn’t make the assumption that your baby is named after robin, and you can always explain your reasoning behind choosing rueben, if anyone wonders. good luck! 
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Keep the name you’ve always liked.
“Not my monkeys, not my circus” is a useful mantra when it comes to other adults. If your sister chooses to make a fuss over something, let them. Only impacts you if you let it.
After all, after the baby is born, all the hubbub over naming will die down. Ppl will see a baby they love and get on board with the name or simply get over it.
Absolutely name him [name_m]Rueban[/name_m]. And don’t let anyone stop you. And dobt consult anyobe close to you. They cant always fully appreciate or understand what it means to you. After this long knowing youd want this name ut becomes like a spiritual connection. No person or thing should take that away from you. Dont say anything, just do it, make no apologies, and savor the beautiful time with your newborn and not worry too much. Everyone will adjust as needed, if needed. Congrats to you!
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I think you should use it. If your sister feels uncomfortable I think you can explain (again) that you’ve always loved the name and even say that you’ve come to feel it’s even better now, as it can be seen as a little nod to her coming out. Either way - use the name! It would be one thing for siblings but aunt/nephew the vast majority of people will never even make the connection.
Those are two completely different names. I wouldn’t sweat it, go for it!