No, you can't disable the interior weather. That's cutting half this mod away.
As for 'ambient' lighting being unrealistic because it's all-pervasive, that's the whole point of ambient lighting. Directional or point lighting is the type that should be blocked by meshes, but ambient is the type that is everywhere. So I'm not entirely sure how you could have a problem with it being everywhere.
The lighting is balanced so as to not appear too bright. If it is too bright, it's probably because it was designed mainly for use alongside Real Lights. I'm not really following your problems, you say it is too dark with Real Lights, but then it's too bright without it.
If you only want weather sounds inside, then perhaps Storms and Sounds is more what you're looking for.
Its dark with RL at night, but bright when day with RL or without. Its not excessive brighting problem. Directional sunlight isnt blocked by meshes for Oblivion engine (or any other engine without realtime shadows support for objects or lightmaps or raytracing (raytracing isnt for realtime for modern hardware of course)), its going trough them. Look at the brighter, than in vanilla game, floor and some walls in your mod - its from directional light.
I'll show it.
Vanilla:
http://i47.tinypic.com/21kl2.jpg
http://i48.tinypic.com/2vbtrw5.jpg
All Natural:
http://i50.tinypic.com/kby4hl.jpg
http://i49.tinypic.com/344ce9e.jpg
All natural + RL:
http://i50.tinypic.com/2eolc28.jpg
http://i47.tinypic.com/2z65iz9.jpg
Thats why its a mistake imo to add directional sunlight for Oblivion interiors. If only engine has realtime shadows or lightmaps, that would work. But sadly not in this case.