For me, cydia has been a stable, usable and fully open-source package manager and 'nix subsystem. It has solved all of the problems I had that were due to the shoddy (but usable, to be fair) implementation of the BSD subsystem and it is happy to coexist with the buggy, closed-source installer. As soon as the last few games that I manage through installer make it over to STE's cydia source, I'll be losing installer for good.
As for cydia, I don't know how to uninstall it. Nor do I care to find out.