6 years later and two VPS later, I decided it was time to leave Phusion Passenger.
I was experience several downtimes due to database (both mariadb and mysql) crashes. It turns out the database could not recover because ruby was occupying the whole memory (512Mb on DigitalOcean). The solution was to shut down apache, then start the database, and finally start apache again. But this would only work for a couple of days.
I decided to move all my django sites to WSGI (yes, I was deploying django apps using passenger) and ported a sinatra app to django (thanks to legacy database support) just so I could get rid of ruby.
It all works well now. But in the meanwhile, I went to read Passenger’s source code and I am currently considering forking and removing everything ruby from it. Just an apache2 module that would automatically handle wsgi, avoiding 4 lines of apache config per project. It can be done, I am just not sure it is worth the time. Maybe it would help other people with plain-simple deploying on Apache/NGINX?