Revert "Audit uses of IsRunning and GetState"

This reverts commit 72cf2bdb87.

SYSCONF settings are getting cleared when they shouldn't be. Let's
revert the change until I get proper time to figure out why it's broken.

Source/Core/DolphinQt/Debugger/ThreadWidget.cpp

@@ -258,7 +258,7 @@ void ThreadWidget::Update()
 
   auto& system = Core::System::GetInstance();
   const auto emu_state = Core::GetState(system);
-  if (emu_state == Core::State::Stopping || emu_state == Core::State::Uninitialized)
+  if (emu_state == Core::State::Stopping)
   {
     m_thread_table->setRowCount(0);
     UpdateThreadContext({});