You might have missed out on a few other factors. The separation of inode from file name in a directory enables hard links, but I doubt that hard links constitute the only, or even the original, motivation for that separation.
I have a copy of "The Bell System Technical Journal", July-August, 1978. This is one of their special issues, and it's titled "Unix Time Sharing System". That's the place where Thompson, Ritchie and company published their description of version 6 and 7 Unix, and what you could do with it.
I see descriptions of inodes and the file system, but no motivations for the design. Ritchie and Thompson note that a
create (their spelling in the BSTJ) system call makes the inode and sets the values, while
open system calls fill in OS table(s) that can hold inode data on further file accesses.
One of the key paragraphs talks about the chunk of disk holding inodes, which they called the i-list:
The notion of the i-list is an unusual feature of UNIX. In practice, this method of organizing the file system has proved quite reliable and easy to deal with. ... It also permits a quite simple and rapid algorithm for checking the consistency of a file system, ... This algorithm is independent of the directory hirerarchy, because it need only scan the linearly organized i-list.
The original designers found that keeping inodes seperate from data made things more reliable.
I believe we can point to years of experience making that true. MS-DOS and other filesystems where the directory hierarchy is all mixed up with the allocation (FAT) are pretty fragile. If a sector in the FAT goes bad, things are really difficult to recover. But if a sector in a directory goes bad, then the inode, somewhere else on the disk, is still around, with a link-count that indicates it belongs to some directory, and thus can be recovered.
It looks like maybe the obvious overhead of looking in a directory for an inode number, then looking in the inode for permissions or data is compensated for by either making the OS handling of files simpler, or by greater reliability.