RTF is a global modification that replaces all towns in the game.

I would make it so they worship spirits like the Orcs, but some kind of evil spirits (which is why they don't get along with the Orcs). For example, some powerful water spirit from the spirit world.

In general, I see the Lizardmen as a neutral faction that seeks balance in the world/is detached from it, rather than allying with the Orcs because their soul (like that of the Nagas) is inclined towards creation. On the other hand, they could easily be made into an evil faction.