I don't think there is a choice in that - it's allow popups or use some kinda adblocker software to choose but that in itself will require daily maintenance to block other popups. I doubt Mozilla here can do much to help with popups unless the pops matches a database of known malware infected site or sites posing as legit sites then by the metrics will block it but beyond that Mozilla won't step into this mine field.

Popup blocker exceptions are considered site permissions, and they are stored in a SQLite database. So unfortunately it's not a simple matter of setting a preference.

One possibility would be to investigate a toolkit like CCK2 from Mike Kaply. https://mike.kaply.com/cck2/

If you haven't already, you might want to join the Enterprise mailing list to tap into your peers' knowledge. See: https://www.mozilla.org/firefox/organizations/