IMO (and that's all it is), it doesn't matter how rare the name is, like so many others are fixating on.
Think about your sister's husband.
His father has died, and I assume relatively young if they're having babies. This must have been hugely upsetting for him, and the loss of a parent is something that is really difficult to get over - if we ever do.
Naming your child after them is the perfect solution, as it's a little piece of them through generational genetics, and now he carries the honour of a name. My brother is named after his grandad too.
It is not fair for you to expect them not to honour his father - who had been in his life since he was born - just because your ex who you've known a couple of years was/is a shit dad and partner.
I understand it will be odd saying and writing his name so much, but it's something you need to get over.
If this is feeling like a huge issue to you then I (without any sarcasm or judgement whatsoever) suggest you get some kind of counselling for the feelings you hold about your ex, because they shouldn't cause a reaction like this, and certainly shouldn't come between you and your sister when she has a brand new baby nephew for you to bond with.
The only thing that you might be a little annoyed at is why they didn't warn you about it - but I think it's perfectly reasonable for them to simply not realise that it would bother you.
My ex abused me for 6 years and reduced me to a shadow of my former self. I would be happy to be able to associate that name with a lovely baby instead of those horrible times, to be honest. New beginnings and all that.