There is a way to customize which groups can see each other's threads in a group discussion board.

Restrict Topic to Selective Groups

1. Navigate to Communication tab and select Discussions.
2. Find the topic and select Edit Topic from the drop-down menu.
3. Expand the arrow for Availability Dates & Conditions and select Manage Restrictions.
4. Select Restrict topic.
5. Expand the list by clicking the arrow next to the group name.
6. Check the boxes for the groups you want to participate in the discussion board. Note: If you select all groups, the discussion board will be open, allowing everyone to view and respond to each other's threads.
7. Click the Add button.
8. Click Save and Close.

Video Walkthrough