Fundamentally there really aren't issues with large folder trees. I dogfood ST on a daily basis with projects of around 100k files and regularly work on the syntax definitions, where saving a syntax definition triggers reindexing.
We made a tweak in 3125 to the default number of workers that should address users who don't care for fans spinning up on their laptops.
Sublime Text already sets indexers as low priority. While it is true that the indexers will use spare CPU, it shouldn't really "take over" unless the OS has trouble scheduling. Our tweak to the default number of indexers should help reduce this symptom.
The Console shows errors in indexing, to allow the user to find issues with syntaxes. The progress of indexing is displayed in the status bar, and there is a new Index Status window in build 3125 allowing users to see exactly what is going on.
We've got some ideas about further ways we can make the indexing process even more robust.
One of the best ways to help ensure that betas don't run into situations like we are discussing here is to help test the dev builds and help test the third-party packages you use with the dev builds.