You're not paranoid, but there are also lots of advantages to centralization, as the article touching on this in Wired says "Having one central ___location allows people to collaborate more easily" (I'd love to know if anyone has attempted to quantify this).
What to do about it?
* Use other would-be global centralized repo to create competition, eg Gitlab.com (or if you demand 100% FLOSS, maybe notabug.org though it is a very long shot for achieving such centrality)
* Discount centralization benefits and self host, eg using gitlab, gogs (which notabug runs), kallithea, or various other FLOSS code hosting applications
* Work making migration between hosts easier (eg issue and other configuration import/export)
* Work on harder problems of federation among code hosts; distributed bug trackers have been reinvented many times but never taken off, but maybe just the right approach hasn't taken off yet, or maybe there is something in federated social web approaches
* Do one or more of the above and treat Github as marketing and backup for your main platform (or vice versa), analogous to what the indieweb people recommend for dominant social networks http://indiewebcamp.com/POSSE
What to do about it?
* Use other would-be global centralized repo to create competition, eg Gitlab.com (or if you demand 100% FLOSS, maybe notabug.org though it is a very long shot for achieving such centrality)
* Discount centralization benefits and self host, eg using gitlab, gogs (which notabug runs), kallithea, or various other FLOSS code hosting applications
* Work making migration between hosts easier (eg issue and other configuration import/export)
* Work on harder problems of federation among code hosts; distributed bug trackers have been reinvented many times but never taken off, but maybe just the right approach hasn't taken off yet, or maybe there is something in federated social web approaches
* Do one or more of the above and treat Github as marketing and backup for your main platform (or vice versa), analogous to what the indieweb people recommend for dominant social networks http://indiewebcamp.com/POSSE