Lets presume that you have a 3rd party application that just runs a query against the SQL Server. You see in the profiler that the query does not performs well and can see the way to optimize the query, however it is the 3rd party application.

Is it a dead-end or still there are chances to do something about it?

Very nice article here (in Russian language)

P.S. It is also quite funny to read as long as you know Russian language well :)