Hi Kevin- Julianne from Mixpanel Support here.
I hate to be the bearer of bad news, but it isn't currently possible to increase the rate limit for the Query API. The limit is in place to maintain our computing capacity for all of our customers.
The Raw Export API has a higher rate limit of 100 concurrent queries, 60 queries per hour, and 3 queries per second. This can be used to export the raw event data for downstream analysis. Would that work for your use case?