Nikkor 50mm f/1.8 being a very common and inexpensive lens even when new, it makes no sense to send it in for a repair or recoat. It is very unlikely unless it is a VERY heavy scratching, it will affect image quality. I have lenses with light cleaning marks and ones that are pristine. Haven't seen any difference that can be attributed to scratches.
Shaprness and contrast depends more on variations in individual lenses rather than existence of light cleaning marks. I can say this because at one point, I had 3 identical lenses (50mm f/1.8 AFD) all new - and especially wide open, they had significant differences. I ended up keeping one and send it into "repair" under warranty to get it right. (and boy it made a difference)
I *think* what comes down is, wether or not if you can accept lens that are less than perfect and you believe what you paid is worth what you recieved. I am very particular about my lenses. I'd be trying to return it if I wasn't informed ahead of time - even knowing it has no material effect. If you paid very little for your lens, you might just want to keep it. It's hard for me to say without seeing and playing around with your particular lens though.