The “spirit of Stack Exchange” is defined by the about page and the FAQ page. These pages are identical across sites, except for the site name and description, and for the first section of the FAQ (which site moderators can edit). For historical reasons, the content is slightly different on the original Trilogy (Stack Overflow, Super User and Server Fault).
In particular, “Civility is required at all times; rudeness will not be tolerated. Be nice. (…) Be honest.” is in the FAQ on all sites.
Beyond that, when it comes to interpretation of these rules or to additional rules, each site has its own peculiarities. Each site targets a different community, which comes with its own cultural assumptions. This manifests itself in the attitude towards some topics such as homework or suspected non-disclosure agreement violations. It also manifests itself in the use of Stack Exchange features, for example some sites tend to hunt and delete obsolete comments while others delete comments only when they meet a high threshold of inappropriateness (Math.SE is in the latter category).
Without knowing the specific situation, I would guess that the question was locked to still the unending discussion in comments and kept pending resolution in the meta discussion. That discussion has been inactive for a long time, so I guess it's time to move on.
Note that you can flag locked posts; I've done so.