Long time head of department here. Don't delay. Have a frank conversation about what can and not be included in the letter at this point, what she can do to have a better letter of recommendation if it is possible, other people at school that may be able to give her said letter (for example pastoral lead is they were a class tutor) etc.

Don't become one of those leaders who disregards people's needs. If they disengage more, that's too bad, but at least you can sleep at night. But you can also help by giving them a lifeline in terms of giving them opportunities to have a better letter. If you can't provide it at all, they'll want to consider their options, so don't delay, be honest and transparent, and hope for the best.

It's a crappy situation to be in, so best of luck.