I can understand your partner's feelings towards your eldest, to be honest. Those are valid, understandable, and biological feelings.
I was lucky that my partner's eldest was quite interested and lovely to our baby son, although it's worn off a bit as he's aged and got more annoying! If she completely rejected him, I think that would have damaged the relationship between me and her to a level that would have been very difficult to repair. It's not a choice to feel some very strong feelings when your innocent baby is rejected by their own family. It's a very upsetting feeling, and I would have struggled to tolerate that long term too.
It would have spoilt what is one of the happiest and most cherished times for most parents for me. It's likely your youngest has suffered due to the friction in the house, too.
Your eldests feelings were understandable, but at 13 years old I would expect a better level of maturity and therefore behaviour. Ignoring and rejecting an innocent baby sibling at that age is poor behaviour.
What did you do to try to remedy it? If you and your partner both did everything you could to repair things, and you son was really firmly deciding he wasn't part of your new family, then I think it's really unfair for anyone to accuse you of choosing your partner over your son. If you tried your best and your son still rejected your new family, that's on him.
He's almost 18 now and you can have a less parent-child relationship pretty soon. A lot of 18 year olds leave home for university at that age anyway. Support him emotionally and practically as you would any adult child of yours that's left home. The circumstances are now immaterial, feeling guilt about how things are won't improve things.
Personally I think if you leave your partner now it would be extremely unfair on your 4 year old, and your partner.
Work on having a relationship with your eldest outside of your family, stop trying to blend him in, and also work on repairing your new family unit. I actually feel quite sorry for your partner and I hope you can fix things so he can finally enjoy having a family. Sounds like it's been hell for him.