For a simple rename routine, I allways use the “mv” command. It is not dangerous. Teorically, if you use “mv” to “move” a file across a file system, you will loss the resource fork of the file, since it uses really “cp” plus “mv”, according to mv’s man page. For such task you can use instead “ditto”, which will preserve the resource fork (useful for, eg, carbon apps, etc.). See “man ditto” in a Terminal window.
However, regarding your original question:
tell app "Finder" to set name of alias "path:to:file" to ".newname"
At least on my own tests, this method won’t affect the visibility of the file.