Take the money.
She wants to pay you, she wants to formalize this somehow, and I think, if you don't accept the money it will be a harder subject to approach later. And you, too, should be prepared to reciprocate if you need her to watch your son.
I'd also make things just a little more formal by asking her for some emergency contact numbers, (like her spouse/partner's cell or work... in other words, in case she gets stuck and doesn't show up to get her kid... it happens.) Agree upon start and end times.
The only other arrangement that might suffice, if you were both in agreement, is to set up a trade, with each of you keeping track of hours on your calendars. I've done this with two different families and this has worked well. When everyone is keeping track of hours and alternating care days, etc. it seemed to work for us. (And we never let one family or another accrue more time than seemed reasonable. About four hours or so, so no one got stuck doing a full day of care.)