Inhibit SQL Server trigger execution
When the utility runs, just have it (or whatever calls the utility) run this command:

DISABLE TRIGGER dbo.trigger_name ON dbo.table_name;


And then afterward:

ENABLE TRIGGER dbo.trigger_name ON dbo.table_name;


It would be better to have the utility do this just around the statement(s) affecting this table specifically (and wrap that in a transaction), since the trigger is disabled for all users, not just the utility.

Another way - if the utility passes a specific application name in the connection string, or is known to be the only thing connecting as a certain user or from a certain host - is to check sys.dm_exec_connections/sys.dm_exec_sessions within the trigger.

ALTER TRIGGER dbo.trigger_name
ON dbo.table_name
FOR INSERT, ...
AS
BEGIN
  SET NOCOUNT ON;

  IF NOT EXISTS 
  (
    SELECT 1 FROM sys.dm_exec_connections
    WHERE client_net_address = '10.65.10.5' AND session_id = @@SPID

    /* or 
    SELECT 1 FROM sys.dm_exec_sessions
    WHERE host_name = N'MELVIN' AND session_id = @@SPID
    */

    /* or 
    SELECT 1 FROM sys.dm_exec_sessions
    WHERE program_name = N'My Utility App Name' AND session_id = @@SPID
    */
 )
  BEGIN
    -- trigger logic here
  END
END


If the utility logs in as a specific login separate from the main app, then you could say:

IF USER_NAME() &lt;&gt; N'user name' /* or SUSER_SNAME() or ORIGINAL_LOGIN() */
BEGIN
  -- trigger logic here 
END


If the utility always handles multiple rows, and the main app always only handles one row, then you could do this:

IF (SELECT COUNT(*) FROM inserted) = 1
BEGIN
  -- trigger logic here
END


If the utility could call a stored procedure instead of using ad hoc SQL, your life would be a lot easier, because you could lock the table in a transaction, disable the trigger, do your thing, then enable the trigger again. (Having this control is yet another benefit of using stored procedures and not compiling your SQL code into an app.)

If you can't fix any of these things, then you may want to look into disabling the trigger and achieving its goal in some other way. Without understanding exactly what the trigger does, it's difficult to be any more precise than that.