a module can add and remove functionality, but can't change how the very core of anope works... a module that just "rewrites Nickserv and Memoserv" isn't possible as parts of both are handled by the core. You can override/add/remove the parts that are in modules simply by unloading those modules, or having your module override them - but in that case they might as well be unloaded.
And about pointing you in the right way... you haven't even said on how you plan to interface with anope.. an IRC client, xmlrpc, mysql commands, ... Also keep in mind the anope core is single threaded and not threadsafe.
There is/was a misc_sqlcmd module which allows you to give anope commands through MySQL, but it was still under development when the author left. Might be worth looking at...
There is also being worked on a new xmlrpc module for 1.8, however it s quite recent and not even development versions are available yet. This is probably a php-side more complicated solution then MySQL, slower as well, but should allow feedback..
And there are of course other posibilities..