src/Pure/PIDE/prover.scala

--- a/src/Pure/PIDE/prover.scala	Sun Feb 14 13:38:31 2016 +0100
+++ b/src/Pure/PIDE/prover.scala	Sun Feb 14 14:33:32 2016 +0100
@@ -183,9 +183,15 @@
 
   def terminate()
   {
+    system_output("Terminating prover process")
     command_input_close()
-    system_output("Terminating prover process")
-    terminate_process()
+
+    var count = 10
+    while (!process_result.is_finished && count > 0) {
+      Thread.sleep(100)
+      count -= 1
+    }
+    if (!process_result.is_finished) terminate_process()
   }