Most graphics intensive programs (like games) scale, that is adjust to the graphic capabilities of your computer. The program looks at your hardware and sets an optimum level of details.
I run Mozy to back up my files online, in the settings there is a slider to adjust between faster backups and faster computer.
Why not have a similar option for the indexer? During the day you could restrain it to 50% of system resources, it would be slower but it would not render a computer unusable. I've read of people having to put fans on their laptops because the fans could not keep the computer from overheating during indexing. Being able to slow down the index could actually make the process faster if you could prevent complications during the index process.
Finally, I suggest that Logos put an index complexity number on every resource based on how involved that resource is to index (perhaps the number of entries that book adds to the index). Then at the beginning of the indexing process these numbers could be added and a time forecast could be based on how quickly the indexing is working through the total expected number of index entries. This seems to me that it would result in a more usable "time remaining" thus helping to manage the expectations of us antsy users.
These suggestions seem simple enough to me, however, Logos engineers please forgive my ignorance if these are actually huge technical challenges.