Let’s Encrypt is planning to introduce a rate-limit override form for domains that regularly exceed the rate limits. It’s unclear whether your use-case would qualify though, as they haven’t released any details yet.
The IP-based rate limits probably won’t be a problem, I’d imagine you’ll run into the 5 certificates per domain per 7 days limit much sooner. Maybe try a staggered rollout, with one user per day or something similar?