The problem you've got with your current idea of encrypting the salt is merely "kicking the can further down the road" In order to be usable the salt will need to be decrypted, which means the code will have to know how to do the decrypting, when means the developers will know how the code does the decrypting and its parameters
You could, of course, keep the decryption key in a secure string in memory only, never save it to disk and create an interface that lets the company CEO paste the key in (over an encrypted connection) from a USB he carries on a chain around his neck, that has a thumbprint lock.. etc.. and he needs to do that every time the server is restarted..
As per the comments, having a single salt could easily be switched out for a per-user salt, but your rogue dev probably still knows the users who are worth attacking so it might not help much if there are only a handful of them.
You really need to be looking at a hash algo that is a lot slower (devices that do billions of MD5 hashes/sec have existed for a long time), which means that brute forcing the passwords is unviable. There is of course a trade-off with these; they are much more work, computationally, for your server and by deliberately implementing something that is slow and takes a lot of resources you can line yourself up for DOS attacks, that will then need mitigating by separate means.
The immediate solution to your problem, if this is actively happening, is to change all the users' passwords and have them reset them to something else. You can detect if they change them back to what they were before (because the hash of the new will be the same as the hash in the backup table you'll create before you change everything). This has the side effect of letting your users know you've been compromised, but you could window dress that as your "awesome security systems have detected suspicious activity and locked their account for their safety" if you need to avoid revealing you've been compromised. Dealing with the company image fallout of this isn't something I guarantee can be swept under the rug but it's a problem for your marketing department rather than SO..