Why are you trying to avoid it?  It's not terribly difficult.

1. Download said applications
2. Open MKVExtractGUI
3. Drag MKV into MKVExtractGUI
4. Select audio stream
5. Click Extract and extract somewhere
6. Covert FLAC file
7. Open MKVMergeGUI
8. Drag in MKV
9. Drag in converted audio track
10. Untick original audio track
11. Make MKV

Or did you want a one-click-does-all thing?  If so, see if something like Xvid4psp converts it for you.