Obviously its up to you whether you want to tell your mum or not but I didn't tell my mum when I lost my virginity! I think if she knows he's staying over, she can probably guess you are having sex. It makes me wonder why she cried when she found out about your brother if she is so relaxed about letting your boyfriend stay over? She might not flip out as much as you think.
I know some mums and their daughters are quite open about sex, but me and my mum never were, and my sex-life is very much private! You don't have to tell her if you don't want to, and considering how she reacted over your brother I can see why you are apprehensive!
As dipsy said I'm pretty sure you can get the pill from family planning clinics, even if you're under 16.
http://www.fpa.org.uk/ <-------- this is the family planning association's website, you'll be able to find a clinic in your area on here. Even though you are under 16, everything you discuss with them is fully confidential.
You can also go on the pill for regulating your periods or if you are having particularly long or painful periods, so if you don't want to go behind your mum's back but are reluctant to talk about sex, you could always say you wanted to go on it for that reason.
I think you are being very responsible, and although you are underage, you seem to have thought it through and well done on being so responsible and getting on the pill! I think if I was your mum I would be proud to have a daughter who was so clued up, there are so many people out there your age that aren't.