If you have the Enterprise Edition on this site and it is alt least SQL Server 2008, then you could configure the Resource Governor to assist with the situation. I don't have experience with it myself but just know of it and its overall purpose. In the brief internet searches I did I found info from BOL that indicates it will help with throttling run-away queries and allow you to put those queries in a workgroup by themselves, and allow queries in other workgroups to finish quicker via work load priority settings.

https://msdn.microsoft.com/en-us/library/bb895232%28v=sql.100%29.aspx