^Not necessarily. Often times in scientific research, the team leader's role in the research is more administrative; the bulk of the day-to-day research is handled by lower level scientists and graduate students. Carol Marcus would likely have been aware of the group's progress (i.e., which stage is the project in), but there's no guarantee she'd have known about the proto-matter. And based on what we saw of her in the films, I don't think she'd have approved of its use.
--Sran
David comments in TWOK that Carol will be remembered in one breath with Newton, Einstein and Surak, which suggests that she is more than a mere administrator.
Admittedly, David's apparently having a little fun with that comment, so it's unclear that we can take it at face value.