In the end it wasn't too hard to do this manually, based on Stéphane's and xenoid's hints and some prior experience with find.
I had to adapt a few commands to work with FreeBSD's non-GNU tools — GNU find has the -printf option that could have replaced the -exec stat, but FreeBSD's find doesn't have that.

# create a list of "<inode number> <tab> <full file path>"
find rsnapshots -type f -links +1 -exec stat -f '%i%t%R' {} + > inodes.txt

# sort the list by inode number (to have consecutive blocks of duplicate files)
sort -n inodes.txt > inodes.sorted.txt

# remove the first file from each block (we want to keep one link per inode)
awk -F'\t' 'BEGIN {lastinode = 0} {inode = 0+$1; if (inode == lastinode) {print $2}; lastinode = inode}' inodes.sorted.txt > inodes.to-delete.txt

# delete duplicates (watch out for special characters in the filename, and possibly adjust the read command and double quotes accordingly)
cat inodes.to-delete.txt | while read line; do rm -f "$line"; done

In the end it wasn't too hard to do this manually, based on Stéphane's and xenoid's hints and some prior experience with find.
I had to adapt a few commands to work with FreeBSD's non-GNU tools — GNU find has the -printf option that could have replaced the -exec stat, but FreeBSD's find doesn't have that.

# create a list of "<inode number> <tab> <full file path>"
find rsnapshots -type f -links +1 -exec stat -f '%i%t%R' {} + > inodes.txt

# sort the list by inode number (to have consecutive blocks of duplicate files)
sort -n inodes.txt > inodes.sorted.txt

# remove the first file from each block (we want to keep one link per inode)
awk -F'\t' 'BEGIN {lastinode = 0} {inode = 0+$1; if (inode == lastinode) {print $2}; lastinode = inode}' inodes.sorted.txt > inodes.to-delete.txt

# delete duplicates (watch out for special characters in the filename, and possibly adjust the read command and double quotes accordingly)
cat inodes.to-delete.txt | while read line; do rm -f "$line"; done