Our ministry administrator is usually paid through the ministry... due to donations being low at this time, she wants to work and donate her time for a couple weeks...
How do I handle this on the accounting books
I want her to get credit for time worked as a donation to ministry

There are some considerations in this.

If you record her time as wages then you will create a tax liability which you will need to offset by giving her a receipt for her donation so you could pay her as normal and pay the net amount to the ministry after accounting for her normal deductions.

You could simply acknowledge her contribution as a volunteer and not have a monetary component this is surely the employees intention. From a Christian perspective you are undoubtedly aware that God honours the things that are done in private so her gift really doesn't need to be honoured publicly unless she wants it that way (don't let your right hand know what your left is doing)

I would agree that you would in fact pay her and she would then donate the funds back. Issues of pay? Is she salary or hourly?

The issue I see with not paying her, and just allowing her to know, is if things later goes bad at work, and she gets angry, she could have course she worked and was never paid.

Just note it as time off without pay. If she wants to volunteer, or even just 'help out on time off' that's separate.
The reason is if she is injured on the job, you need to suddenly (instantly) get her back on the payroll, and presumably WC and liability insurance. One minute retroactively.