You can't take the entire software commercial, as everything previously released under the open-source license will stay under that license. In the case of EmailEngine, all versions ever released under the AGPL license are still in Github; you can fork and use these freely. It is only the path forward that gets closed when going commercial - users can start paying, can stay indefinitely on the already released free versions, or can take the initiative and fork the project.
Simple. Open source doesn’t mean “free code for life”. Most people try to turn their time into money. Besides, any one of us could fork the project, compile binaries with a novel license check and charge for them. Why not the person who actually added value?
A project is more than the source code though, otherwise the original maintainer could just as well fork the project when taking it commercial instead of continuing to use the original name.
