That’s certainly your prerogative, but if it were me I’d at least put think the original theatrical subtitles (or what’s assumed to be them) in an alternative subtitles folder or something for those that want them, and then just not manage this folder as thoroughly as the main subtitles. Seems a waste to just delete them from the project completely.

Edit: oh, and furigana can be done in AegiSub by making a new line, changing the font size, then dragging the line into place in the video preview pane.