andrea,
I just tried that (replacing all references to rss.php with rss-functions.php), and there's still no love :( The wpmufeed.php that's installed is the unmodified 0.3.1 release.
I have caching enabled, and it does appear to be caching.
-jailshell-3.00$ ls -l wp-content/
total 36
drwxr-xr-x 3 unsilenc unsilenc 4096 Jan 20 10:02 blogs.dir
-rw-r--r-- 1 unsilenc unsilenc 4034 Jan 16 16:57 blogs.php
drwxrwxrwx 9 unsilenc unsilenc 4096 Jan 22 06:26 cache
-rw-r--r-- 1 unsilenc unsilenc 32 Jan 16 16:57 index.php
drwxr-xr-x 8 unsilenc unsilenc 4096 Jan 23 01:08 mu-plugins
drwxr-xr-x 8 unsilenc unsilenc 4096 Jan 21 15:22 plugins
drwxr-xr-x 9 unsilenc unsilenc 4096 Jan 21 12:54 themes
-jailshell-3.00$ ls -l wp-content/cache/
total 28
drwxr-xr-x 15 unsilenc unsilenc 4096 Jan 22 06:36 14fbc36039acaa4bdf9665d81c6913af
drwxr-xr-x 14 unsilenc unsilenc 4096 Jan 19 19:42 5704ea27bc73df808a472e8d785b533e
drwxr-xr-x 19 unsilenc unsilenc 4096 Jan 21 16:52 83e049c92fc390b788b1d0ed0fa8be9b
drwxr-xr-x 50 unsilenc unsilenc 4096 Jan 21 16:23 b5ca8c0fbc880ec7ce11744cdab221a9
drwxr-xr-x 135 unsilenc unsilenc 4096 Jan 22 06:29 badd89be15ec548a3d807554faecc1af
drwxr-xr-x 32 unsilenc unsilenc 4096 Jan 21 15:43 cab638d671cab978b4298d620bd1abab
drwxr-xr-x 16 unsilenc unsilenc 4096 Jan 21 13:37 d17a28080ab86216ff2404d69092d684
-rw-r--r-- 1 unsilenc unsilenc 0 Jan 17 11:42 index.php
-rw-r--r-- 1 unsilenc unsilenc 0 Jan 23 01:06 wp_object_cache.lock