Well, besides the fact that shipgirls are not human, even if they look the part, and have different outlooks on life, there is the point to consider that they are immersed in a human society, with human values, which will shape what fate shipgirls will have.
One thing that's for sure is that Operation Crossroads will not be happening.
Now, there are two kinds of shipgirls, the tsukumogami-like shipgirls, still tied to their hulls, and the summoned shipgirls, which are independent of their hulls. Currently in story, only Utah belongs to the second category. But there is a war going on, and more ships are going to sink, on both sides. That's just a fact of the war.
So, when the war ends, there will be more Summoned shipgirls. Those are easy, as there is no need for hull maintenance, and they can live on just from human food and join society and do civilian or military things as they choose.
Sending a ship to the breakers does not mean the shipgirl dies. It just means she can be summoned later, if there is a need for it. I feel that summoning for the sake of summoning will not work.
So, the shipgirls tied to their hulls are the ones that will pose a problem. Those hulls need maintenance and regular checks against the worst enemy of any steel ship: sea corrosion. The ideal solution is turning them into museum ships, but in a lot of cases that is not practical. You cannot have all the surviving Fletchers as museum ships, for example. The Iowas, for another example, could, because there is only four of them, and they actually were deemed useful after the war.
The solution, which is kind of obvious, is to ask the shipgirl what she wants to do after her hull is deemed not fit for additional upgrades, and not needed for service. I get the feeling that most would choose being scrapped if they are no longer needed, to ease the burden for the military forces of the country.
Shipgirls do have a sense of duty to their nation, and will accept whatever fate the nation decides for them. Asking them is the polite thing to do. But it will be the humans that will be a problem. Some will see scrapping them as murdering them callously and in cold blood. Some won't care, except when it comes to their shipgirl, like sailors that served aboard a particular ship, or had relatives that served on her.