Converting Heap to MyISAM issue

At work we have a problem that has now occurred more then once.

Problem is that query is in state of converting HEAP to MyISAM and it paralyzes our server( query in this state is not able to kill itself and kill flag is not evaluated until only after the operation which seem to take FOREVER in our case)

The following global MYSQL variables appear to us:

| tmp_table_size      | 17179869184 |
| max_heap_table_size |  8589934592 |

Any ideas what we should do?

Should we perhaps adjust the sizes of tmp_table_size and max_heap_table_size to have the same value?

Would that help?