You can get Tweak UI.  Its boot tab has an option to turn off the automatic running of scan disk.

It is one of the power toys from microsoft.

Information about Tweak UI is available at:
http://www.jlilest.com/tweak.html#tweak

Having said this, you should probably think long and hard before turning off the scan disk option.
Without running scan disk you would not find out about damaged files or directories.  As a result you could lose more files or programs.  You might end up having to reformat in extreme cases.