It can't be helped. Civilians are crazy like that. If they see a hostile, they will ram it. Only way out is to use SM mode to put DR high enough for neutral or friendship.
I don't know if you can use the truce timer after starting a game, but try it? Otherwise you could try turning off sensors in sol so no schenanegins happen there.
I'm playing my first multi nation start. 3 player controlled empires on earth. For some reason, two ships from the civilian shipping lines from one of my empires keeps trying to ram another ship from another empire. I'm sure this is some simple thing that I messed up along the way. How can I make this stop?