Update March 2014: As mentioned by cheshire’s answer, EGit 3.3 added that prune feature.
fetch.prune mentioned in
git config can be added to your Egit configuration:
Original answer (March 2013)
EGit perform this pruning when remote tracking branches change (after I fetch).
Not that I know of.
More generally, perform any action after each fetch on the client side is not possible with hooks.
It has been requested, and was at one point implemented on the server side only: hook
post-upload (run after a fetch), but removed, for security reason in a multi-user environment.