From svnkit 1.3.2 changelog:

• Negotiate authorization mechanism was not used when multiple authorization
  schemes were offered to client by server.

I have verified that replacing $HUDSON_HOME/plugins/subversion/WEB-INF/lib/svnkit-1.3.0-hudson-3.jar with the svnkit 1.3.2 jar enables my master hudson to work with subversion repositories protected by Apache+https+mod_auth_kerb(negotiate).

I was warned on the mailing list that this simple replacement might affect the behavior of slaves because Hudson has a modified version of svnkit. This may require more than a simple re-release with a new svnkit jar.