I'm not exactly getting the problem.
You bought a thing. It was new. It has a warranty. The warranty is being honored. It may well have been working when it was put in the box and shipped. Stuff happens.
Legally (in most states), that's all you're entitled to, a warranty repair at an authorized service center.
Some sellers will go the extra mile out of goodwill to take it back. Others won't, or possibly, can't. That's sort of what you get with building a relationship with a local dealer. Or you deal with an online dealer who does a lot of mail order business and will do returns. Or you sometimes find a great price online, but the dealer isn't able/willing to do the return. There's really not all that much profit in guitars these days.
It really isn't that big of a deal, the pickup will be replaced, life will go on. That's pretty easy stuff. If it was a twisted neck or something, that's a big deal.
The dealer you bought it from CAN help by contacting their sales rep at Fender to see about expediting the part to the service center doing the repair.
I can say, my experience with warranty service from Fender and other manufacturers is a joke. I once bought a Custom Shop guitar. Logo decal wasn't applied properly and the edge was lifting, right from the start. No big deal. Fender fought it tooth and nail like it was the end of the world. A freaking water-slide decal, on top of the finish. Probably cost Fender more to fight with me about it than the 90-cent decal, a 40-cent stamp to mail it and the 0.25 hrs of labor they paid the shop to replace it.