I think the only way to change the algorithm to something other than MD5 od DES wouold me to tinker with the source code.
However, doing that is not neccessary. Although vulnerabilities have been found in both algorithms, they do not apply to the way these algorithms are used by shadow. MD5-shadowed passwords definitely cannot be recovered. You can check if you are using MD5 by looking for the string $1$ after the username. Here's an example from my /etc/shadow (slightly changed, of course):
I suggest you do a google search on "md5 vulerability" and the shadow program.