For the OP, not doing organized sports since age 12 isn't fatal but it puts your DD very much behind the 8-ball. I won't quibble with her decisions to date b/c what's done is done and I'm sure she is extremely successful in her chosen path. But you're now looking at being competitive in applying to a SA.
SAs view sports are about more than just physical prowess. SAs view sports as being about teamwork, striving to a goal, sacrificing for others -- and that, to at least some extent -- the athletic "field" is a model for the battlefield. There is a reason that 92% of admitted students were varsity athletes. That does't mean the other 8% didn't participate in sports, only that they weren't varsity athletes.
As a poster above noted, sports are VERY much a part of all four years at USNA, and Admissions tends to be wary of someone who hasn't been involved in sports -- what if they don't like it? What if they can't maintain physical fitness on their own for 4 yrs? [As an aside, without organized sports, your DD should be running a 7:00 or better in the CFA -- where, as you know, the mile comes at the end of a series of events; she really needs to approach the max score in every event].
If your DD's heart is set on USNA, I strongly suggest she take some time this summer and participate in organized sports. There are all sorts of summer leagues and sports camps, etc. I'm sure she's very busy with other things but it all depends on how much she wants USNA. Even better, do it in the fall as well, whether in school or outside of school.
No doubt someone will post that "I got to into USNA" or "my kid did it" with no sports. I've also no doubt there are such individuals at USNA. But you're probably talking a handful in each class. The question is, do you want to be competing for one of those handful of spots or one of the 1125+ spots taken up by athletes?