Kotyan (You’re just running for your life), Le Loi (as you said), Ivaylo (Fighting peasent-crushing feudalism before it was cool), Jan Ziska (fighting peasent-crushing theocracy before it was cool).
All of these can argue for the top spot of morals.
For runners-up: The other 2 Dawn of the Dukes campaigns are also pretty heavy on “protecting your people from the tatars and teutons”, so you’re the good guy there too.
Joan is a legendary case of this, so her too.
El Cid plays this way, taking on both the Muslims and Christians to bring peace, though gets alot of flak for its historical inaccuracies so while you’re the good guy in the campaign the events represented are a bit sketchier.
Under that I’d put the “self defense in a power struggle” cases; where you play as a monarch against internal opposition, so Sundjata, Bayinnaung, Most of Bari, most of Prithviraj.