It has to be said, anyway, that tampering with an INI text file (related to a single application) is potentially quite less... dangerous than tampering inside the main OS registry...
From a security perspective, pushing users to edit the registry is hardly a good thing, in my humble opinion.
Maybe the INI file could be kept just for those custom settings which are not managed by the GUI.
Most users (those who do not want or need to go beyond the GUI) would take advantage of the performance gain (if any) due to the registry integration, while the "few" others would create a little text file with negligible effect on performance.
Or maybe those custom settings could be written by the user inside a dedicated GUI window, with no need of file (or registry) editing at all...