Best Practice for closing a blocking connection to the database.

Background:
Using toplink/eclipselink to manage the the connection to the database.
We support 3 databases, Oracle, Mysql, and MSSQL.
We host the an application locally (SAAS) and we also distribute it to our clients so they can run it on premise.
Problem:
From time to time the application will execute a route that query the DB and will take 10+ minutes. When we find these queries we generally fix them, but it takes time to fix the problem and roll new code to production. We have also found that if an end user executes the query to many times they can potentially bring the service down - maxing out the database connection, or putting a huge load on the DB effectively rendering the system to a crawl.
During this time period the IT team need a way to abort a transaction. The current approach, for our SAAS solution, to scan the database find to the long running query and kill it. The application is smart enough to recover and everything seems to work fine. This doesn't always work for our on premise customers - often they don't have a DBA or adequate resources to monitor the system. Therefore, I'm looking for a way to have the application kill/close any query that is lasting longer then X minutes. We currently track the duration of every thread so I can get the time the thread has been actively running.
Stack Trace
Currently we keep track of how long each thread is running waiting for a response from the database such as the stacktrace below, I would like to grab the connection and physically close it. Since we are using a java socket and it's in a blocking state there is no way for us to interrupt the thread. The only option is to wait for it to receive a response from the db - kill the sql process - or to close the java socket.
java.net.SocketInputStream.socketRead0(Native Method)
java.net.SocketInputStream.read(SocketInputStream.java:129)
com.mysql.jdbc.util.ReadAheadInputStream.fill(ReadAheadInputStream.java:113)
com.mysql.jdbc.util.ReadAheadInputStream.readFromUnderlyingStreamIfNecessary(ReadAheadInputStream.java:160)
com.mysql.jdbc.util.ReadAheadInputStream.read(ReadAheadInputStream.java:188)
com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1931)
com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
com.mysql.jdbc.Connection.execSQL(Connection.java:2998)
com.mysql.jdbc.Connection.execSQL(Connection.java:2927)
com.mysql.jdbc.Statement.executeQuery(Statement.java:956)
org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.executeSelect(DatabaseAccessor.java:854)
org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.basicExecuteCall(DatabaseAccessor.java:573)
org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.executeCall(DatabaseAccessor.java:501)
org.eclipse.persistence.sessions.server.ServerSession.executeCall(ServerSession.java:536)
org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeCall(DatasourceCallQueryMechanism.java:205)
org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeCall(DatasourceCallQueryMechanism.java:191)
org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeSelectCall(DatasourceCallQueryMechanism.java:262)
org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeSelect(DatasourceCallQueryMechanism.java:244)
org.eclipse.persistence.queries.DataReadQuery.executeNonCursor(DataReadQuery.java:188)
org.eclipse.persistence.queries.DataReadQuery.executeDatabaseQuery(DataReadQuery.java:144)
org.eclipse.persistence.queries.DatabaseQuery.execute(DatabaseQuery.java:664)
org.eclipse.persistence.queries.DataReadQuery.execute(DataReadQuery.java:130)
org.eclipse.persistence.internal.sessions.AbstractSession.internalExecuteQuery(AbstractSession.java:2243)
org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1181)
org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1165)
org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1125)
Question
What is the best way to grab the connection and close it - from another thread?

The reason for changing the namespace is to guarantee that they appear as different versions. The namespace is part of the strong name of the DLL when deployed. Yes they will be deployed to separate servers because a server can only belong
to one farm. But when you are doing a migration it won't be clear that you need to install the 2013 version since the .DLL will report that it exists in the 2010 farm already. It will work without changing the namespace, but it would be best to differentiate
versions at that level to avoid confusion.
Paul Stork SharePoint Server MVP
Principal Architect: Blue Chip Consulting Group
Blog: http://dontpapanic.com/blog
Twitter: Follow @pstork
Please remember to mark your question as "answered" if this solves your problem.

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