Company imposing financial penalty for resignation

I understand this is a long shot but the reason cited for resignation was COVID as I would no longer be able to perform the job tasks effectively with my own children now needing more of my time. Do you feel these current times would have any bearing on the outcome of this situation?
Do you feel these current times would have any bearing on the outcome of this situation?

No. As an online teacher you wouldn't be exposed to Covid on the job nor would your be exposing anyone else. Your childrens needs are never a good reason for missing work. Women in the working world learned that decades ago. Besides, if you teach online from home you can be with your children all day long.
But part of the problem here is that $39,000 was the salary from September 2019 to August 2020. So part of this "penalty" relates to pay from last year as well as this year. How that would affect the determination of whether the OP is still considered exempt from FSLA overtime rules, I don't know.

The OP might still be subject to the penalty either way; the question would be whether the penalty would then make the OP eligible to make an OT claim. And unless the OP had overtime, that wouldn't make a difference.

True but it could also be argued that the repayment would be for the last checks the employee was paid and in that case he would be reduced to a pay rate less than the minimum wage. Which isn't allowed.

If a person makes minimum wage and you deduct anything other than the FLSA authored deductions for things like taxes, CS and group health you the employer is in violation.

I had a client, a daycare, that required minimum wage employees to either ware scrubs that they purchased on their on or much cheaper company t-shirts they bought from the employer (at cost). I warned her that since virtually all the employees were min wage that any deduction would be a violation. Sure enough about six months later in comes the US DOL and requires repayment of the t-shirt costs.

The point is that the $3900, if taken out during the last paycheck or two reduced the OP to below minimum wage for any hours worked in a pay period it would be a violation.