You could run the scheduled tasks as a different user, that way they will no interact with your normal account's interactive desktop at all. This certainly seems to work on the Windows2003 servers I administer. Just be careful to make sure that file permissions and other authentication details are set such that the tasks can access what they need to when un as this different user.
Edit: Or instead of running a console tool directly you could have a small script that runs it using WScript.Shell.Run with the "minimise, no focus change" option:
' sample script: c:\scripts\test.vbs
Set WshShell = WScript.CreateObject("WScript.Shell")
WshShell.Run "c:\location\of\tool\utility.exe", 7
then run this with the task scheduler (the command line being something like wscript c:\scripts\test.vbs) instead of calling the tool directly. You should be able to call batch files and other scripts that way too. There is also a "completely hide" option (replace the 7 above with a 0), though in either case the hide/minimise only controls the initial window: if the tool opens more itself then they may still steal focus as before.
See http://msdn.microsoft.com/en-us/library/d5fk67ky%28VS.85%29.aspx for a full list of options for the run method.