We use the free API for a simple 501C3's map. Usually our geo-coding usage is quite low, but a change we made [oops] triggered all >2500 records to re-request.
We can wait the 24H "timeout" imposed.
Our concern is will Google log this as abuse? Do we need to write code to cap our geocode usage at 2499/day in case of a future event?
Google doesn't consider daily over quota as abuse. You can trigger anti abuse systems in case if you are sending too many queries per second from the same IP address as far as I know, but if your QPS is within allowed 50 queries per second you should be OK. Daily quota is reset automatically, so you should just wait until 0:00 PDT when the reset is typically happen.