Reorder MainNoGUI shutdown

Before this change I always got this when closing dolphin-emu-nogui:
```
X Error of failed request:  BadWindow (invalid Window parameter)
  Major opcode of failed request:  10 (X_UnmapWindow)
  Resource id in failed request:  0x3400003
  Serial number of failed request:  215
  Current serial number in output stream:  219
terminate called without an active exception
Aborted
```