Sorry if I'm late to the party and somebody's already said it, but you fucked up OP. I get what you tried to do, and something should have been done, but that's not how you handle that situation. Not even close.
You shouldn't have made a big fiasco over the phone, you shouldn't have allowed your mom to get involved, and you shouldn't have let her know the contents of the phone when you yourself promised your sister you wouldn't.
She's young and you don't want her getting involved with guys like that, I get that, but explain that to her: make her understand how you feel about that kind of behavior (don't use words like disgusting) and talk to her about sex for fucks sake. Don't shut her down or cut her off from other people, teach her how to deal with guys and sex related subjects. The former won't work, and will only lead to problems later on.
I doubt you have much sway now that your parents are involved, but be there for her. If nobody's done it yet, try to talk her through dating, puberty, sex... It doesn't matter if you're comfortable with it or not, it's for the best, especially if you live in America. Sex education is near worthless there and every kid I knew growing up learned everything they knew from other kids and T.V.
In regards to how this specific situation affects your sister, you better do everything in your power to get her trust back. I've got a younger sister who's 13 and I can't see her trusting me with anything for a long time; I've got family I couldn't trust for years because of stuff like that, to the point where there are chunks of my life where people I love don't exist. I'm not saying you shouldn't tell others if you really have to, but don't pretend you'd never tell anyone the things she finds personal enough to share with you alone; be upfront and do your best to be honest. You're her brother, not her father.
All of this comes with the caveat of me not knowing you or your family or the type of place that you live or the type of kids in your area. I'm just assuming, and saying these things based on my opinions and experiences. I'd consider my family atypical and my mother's approach to parenting (especially when I was around your sisters age) bordering on ethically wrong, so I'm crazy biased. Even if I disagree with what happened, you still acted on what could have been a terrible situation. Sorry if this comes off really general or abrassive. It's hard for to talk about stuff like this as it's personal, let alone dance around the fact that I know next to nothing about your lives.
tl;dr: You shouldn't have done that, but it's good that you did something. Be there for your sister and try to earn her trust back. Even if you're uncomfortable try and talk to her about sex, puberty, dating... or get you trust if your mom hasn't (especially if you're in the US). Don't disengage her from a social life or keep her on lockdown, teach her how to deal with guys and the like....
EDIT: One more thing, find out what kind of "relationship" she had with the boy. I know it may seem like he's trying to go pretty far, but a lot of the time it's just talk and "boyfriend" is just a title, especially in middle school.
EDIT 2: Ignore the first edit. I re-read your post and that's not just talk. Keep an eye on that boy.