Is deposit I-539 the easiest way to extend your stay right now?
Yes. It is also the most difficult way. This is the only solution.
More seriously, there could be some sort of amnesty or other program offered to non-immigrants to the United States who are affected by the pandemic. If this happens, it could save you a few hundred dollars.
But I wouldn't count on it. I certainly haven't heard of it, and the current administration is deeply anti-immigrant, so it's unlikely to happen without political pressure.
In terms of risk analysis, the application fees will be well spent.
If so, is it possible to waive fees due to the plight of the Corona virus?
Asking for a fee waiver will make it look like someone with financial problems, which will have a negative impact on their application as well as on future applications for admission to the United States. I wouldn’t do that.
After filing I-539, should she wait for approval to continue her stay? Or is the receipt sufficient?
Once the application is filed, it can remain until it is refused or, if granted, until the end of the extended stay period granted to it.