You can try to temporarily disable Spotlight, removing its files and then reenabling it.
The process to do this involves executing Terminal commands, so please pay attention and triple check each step.
Open a Terminal.app (/Applications/Utilities/Terminal.app) and type:
cd /Volumes
ls -l
Examine the output of that, one should be your “broken” Volume. Once you have it identified, proceed with these steps, all in the Terminal. The first time you execute a command, your password may be required, this is normal.
The output may look like:
lrwxr-xr-x 1 root admin 1 Sep 2 12:23 MacintoshHD -> /
So the name you’re after is “MacintoshHD”.
Step Number One: Disable Spotlight for your Drive.
sudo mdutil -i off "/Volumes/the_name_you_have_identified_before"
Step Number Two: Remove the indexes from the Drive.
sudo mdutil -E "/Volumes/the_name_you_have_identified_before"
Step Number Three: Eliminate all Spotlight Files from the Drive. (two commands)
cd "/Volumes/the_name_you_have_identified_before"
sudo rm -fr .Spotlight-V100
Be careful with the last command, make sure you type it exactly as it appears.
Step Number Four: Re-enable spotlight in the Drive.
sudo mdutil -i on "/Volumes/the_name_you_have_identified_before"
Now this should trigger a Spotlight complete re-indexing. You have to be extremely patient with it. Spotlight sometimes appears to be frozen but it’s really indexing. It’s best to leave it overnight and be patient.
Apply it to the volume, not a directory:
sudo mdutil -i off /Volumes/TimeMachine/
Substitute TimeMachine with the name of your backup volume, of course.
For example...
Johns-iMac:~ john$ sudo mdutil -i off /Volumes/Time15/
Password:
/Volumes/Time15:
2015-10-27 12:37:18.436 mdutil[56686:26121199] mdutil disabling Spotlight: /Volumes/Time15 -> kMDConfigSearchLevelFSSearchOnly
Indexing and searching disabled.
Which does leave the subdirectory reporting as "enabled", but (until proven wrong I understand) the setting at the volume level will override.
Best Answer
You cannot configure how fast Spotlight will index files. Normally, it should auto-throttle itself and not cause massive CPU usage (unless fully rebuilding indexes or doing first-time indexing).
If you run into trouble with Sophos and Spotlight, you could tell Sophos to ignore Spotlight's metadata folder. Also, note that there a lot of grief about Sophos interfering with spotlight: https://discussions.apple.com/thread/3562174?start=0&tstart=0