In general you cannot override classes that are part of the implementation of the web container unless they were designed for this such as a jaxp based xml parser. If you find that you cannot scope classes from the associated service, then your only option is to upgrade the classes from that service to see if its compatible with the newer version.
I actually dropped the digester jar into my server's lib directory and everything seems fine. Are there some issues I should look out for while doing this?
AFAIK, the digester is backwards compatable so I would hope it wouldn't matter too much.