I think this may have came in v6.0 but it is certainly is v6.5. you have the ability to select where the .pat file (index files) are stored rather than locked to the project folder. This will allow you you keep project folder size to just project/bins/settings.
If you still want to disable PhraseFind, both it and ScriptSync have their own license so you can disable the PhraseFind license and keep the ScriptSync active.
Just for reference for those of you who are curious; the PhraseFind index files (PAT files) are only 5MB for every hour of content regardless of video format. This will give you a better idea of how and where to manage these files when starting a project.
ScriptSync on the other hand indexes the files and sync relationship between written and spoken words, but keeps the sync result as part of the ScriptSync interface. So the PAT files themselves are only temporary and do not remain on the system. This is why a script/transcript that has been indexed can move from system to system once the process is complete.
Perhaps in a future update, for users who have both ScriptSync and PhraseFind that Avid allows ScriptSync to do its thing from all the already indexed audio making that process near instantaneous rather than just the very very fast indexing/sync it is doing now. ;)