Malta is essentially selling EU-wide* permanent residency permits and is making mad money out of it. Greece is in dire need of money, and is also entitled to the issuing of EU-wide permanent residency permits, so it makes sense for Greece to follow suit.
* Technically speaking, Schengen-Area-wide.
No, it's actually EU-wide. An EU citizenship doesn't grant automatically grants you access to the labor market of e.g. Switzerland and Norway (both Schengen but not EU) but it does to the UK and Ireland (both non-Schengen but EU).
The Schengen treaty only is about to things: No passport checks on the border and joint police work. It doesn't grant any additional residency rights for citizens.
Which may not be for long if the EU decides it doesn't like Malta selling EU-wide residency permits.