The "right" way is to accept that privacy-conscious visitors reject your use of third-party tracking, and if you really need to track their visits you must use a first-party tool (Piwik, GoAccess, plain old logfile parsing...). It may not seem fair and it may be frustrating, but blocking third-party tracking is just so easy and anyone who cares about privacy can do it with minimal effort.

As a side benefit, when you start doing your own tracking from server logs, you gain valuable insight into where the gaps in data are from the third-party trackers, and precisely how many visitors are under counted.