As you probably know, there is massive corruption in Kenya (I've lived there in the past). This is an EXTREMELY sensitive situation, and she should avoid speaking to any local Mombassa-based authorities, including the police, who could well be bribed by the people at the orphanage to 'make the complaint go away'. Your friend should contact the UK High Commission (it's not called an Embassy in Kenya because it's a Commonwealth country) in Nairobi and take their advice. While the UK cannot intervene in a potentially criminal situation in Kenya involving criminal acts not directly affecting a British person, they may be able to advise her on which Kenyan authorities she could safely report the situation to.
As a foreigner living overseas she should already be registered with the UK High Commission. If she has not, that is potentially damaging her own security. Eg. when the tsunami happened in Thailand, lots of British people (often young, backpackers, casual workers) were living there who hadn't registered with the British Embassy in Bangkok. Those Brits went missing or died, and their parents were desperately calling the Foreign Office and UK Embassy for information on where their children were, or Brits weren't able to be expatriated on emergency flights because nobody knew they were in the country in the first place.
She can register with the UK High Commission in Nairobi by simply texting a special number from her mobile phone - details here ukinkenya.fco.gov.uk/en/help-for-british-nationals/living-in-kenya/registering-with-us
SMS text number for registering is here - ukinkenya.fco.gov.uk/resources/en/word/12424943/sms-consular-registration
If something happened in Kenya, either a national disaster, or even a war (Kenyan troops are currently deployed to neighbouring Somalia not far up the coast from where your friend is, there have been kidnappings from Mombassa by Somali pirates, etc etc etc) and British people had to be evacuated or accounted for then the Foreign Office would have no record of your friend.
Support for British nationals living overseas: www.fco.gov.uk/resources/en/pdf/2855621/support-for-british-nationals-abroad.pdf
Hope I don't sound too alarmist, and this is useful for your friend!