It is not allowed under employment law to give a bad reference - since the legislation came in, the (large) company I work for only gives 'off the peg' references that confirm the period of employment and job title of the person - they say nothing about suitability for jobs, attendance, attitude, etc, as it's far too easy to fall foul of the law. So don't let future reference worries stop you speaking out. Is there someone higher than your boss you could speak to, even if it's after you've resigned? Unless she is the company MD/owner, SHE has a boss who should be made aware of what is happening.