Well, I remember once that when the civil war was well underway (I was playing as the Brutii), as I had conquered Messana and Capua from the Scipii. Then I was able to get the Julii to accept a ceasefire, wich automaticly made me neutral with the Scipii and the Senate too.
The next turn, the neutral Senate gave me a senate mission wich ordered me to hand back Capua and Messana back to the Scipii, or else I faced a financial investigation.

So it is possible for a neutral senate to give you orders. Strange thing about your example though, if an ally of yours attacks another one of your allies, you should get a message prompting you to chose between one of them. And IIRC, a Roman house attacking someone should automaticly end all alliances between the defender and any Romans. Weird thing...