Sorry to hear that other kids are ignoring your daughter -- I agree, those years are tough!
Obviously making friends is the ideal in this case, but that's a process - worth it, but hard if she just can't find a person to "click" with yet. Since middle school is usually when lunches tend to become more flexible, could she eat in a classroom with one of the teachers -- maybe one or two days a week, for example - so that she isn't pressured every day too find somewhere to sit? Especially if the guidance counselor is really nice, maybe your daughter could ask her - and it's still a way to practice social skills. YMMV, but around here it's not common but definitely not usual for kids to just sort of hang around certain classes for lunches. Many kids are in there for schoolwork, anyway.