Tricky. A couple ideas (untested):

1. Delete $INC{$filename} (where $filename is the conversion of a bare module name to a filename) and then re-require the module to re-load it. (You may need to silence redefine warnings.) See require for details.

2. Require the real module and mock an empty subclass instead. (Though you might wind up with un-mocked behavior if you call a non-mocked, inherited method.

sub setup : Test(setup) {
  my ($self) = @_;
  my $mockClass = Test::MockClass->new('Mock::DateTime');
  $mockClass->addMethod('now', sub {'XXXX'});
  require DateTime;
  @Mock::DateTime::ISA = qw( DateTime );
}

sub test : Test {
  my ($self) = @_;
  ok(Mock::DateTime->now);
  diag(Mock::DateTime->now);
}
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