Well, WIC is run a little differently in each state (and the info provided by an individual office may vary a bit from how it's presented in another office in the same state) so it may be easiest for her to ask the office she plans on using to see if they can tailor the package for her...
That said, I was on WIC for about a year in NY (two years ago). We had the breastfeeding mama package as well as the infant package. I am allergic to fish but still had to "take" the tuna that is included in the breastfeeding package and we don't drink dairy due to lactose intolerance but we still had to "take" the milk included in each package. I asked if we could substitute more beans or cheese for the milk and/or tuna and they said no. They did say that WIC was trying to find a way to customize packages for allergenic participants but it wasn't there yet so maybe this has changed in the past year or so.
In NY at the time you had to get everything listed on your "ticket"... you couldn't decide NOT to get an item if it was part of your package. However, other states let you pick and choose a lot more (and I don't know the current NY guidelines). Although they do say that the food should only be used by the WIC recipient they certainly don't check up as such... so if the rest of the family will eat beans, or tuna, or peanut butter, or eggs, or cheese, or whatever then it is certainly worth it. DH ate a lot of tuna that year.

I think mostly they want to make sure the food isn't being re-sold.
And many states now let you use WIC tickets/coupons at farmers markets. Which is very cool. (and around here a number of CSAs have discount memberships for families that are on WIC so that might be worth looking into as well... these specific CSA memberships are only for people on WIC so even if the WIC foods aren't a perfect match for her family it may be worth it if you can then find a discount CSA)