As it states right at the top of /usr/share/pipewire/pipewire.conf:
# It is also possible to place a file with an updated section in
# /etc/pipewire/pipewire.conf.d/ for system-wide changes or in
# ~/.config/pipewire/pipewire.conf.d/ for local changes.
Note what function each property is a part of and reproduce it in your custom pipewire.conf. In your case, it might look like this:
context.properties = {
default.clock.allowed-rates = [ 48000 ]
}