As of FogBugz 7.1.15, licensed FogBugz customers can do this:

Adding a string value named 'pctIndexThrottle' to the FogBugz registry settings (next to sConnectionString, for example) will allow throttling of the search indexer.  Values are interpreted as percentages, so '50' would throttle the indexer to half, '200' would double it, '0' would disable it, '100' is the default, etc.

If you're having this problem in an On Demand environment... you shouldn't be. Please contact Fog Creek support.