SQL Server Temporary Table Security
A #temporary table is only visible from the session that created it.  So even the same user in another session would not be able to see it.  If you load a temporary table in SQLCMD it would be visible to that instance of SQLCMD.  So a subsequent command could load the data into a permanent table, or open a cursor over it and call a stored procedure for each row, etc.

Alternatively you could provision a private schema for the user and load the data into a permanent table there.  Then no other user (other than a database owner or other privileged user) would be able to read it.  The user could then move the data into another schema later.