Ny difference in the First Contact responses

No way you can do this besides controlling the planet yourself. Sectors are completely autonomous and if you already checked "Respect Tile Resoruces" there is no further instruction you can give. The sector AI most likely considers 6 society research worth more than an alien pet (I would as well)

Options you have:

1. Take the pet planet under direct control until the situation on the xenophobic world stabilized and add one of your core planets to a sector for the duration
2. Just deal with the revolts by reducing faction support and doing integration campaigns.
3. put the xenophobic planet in a sector and let it worry about it
4. enslave the xenophobic pop.

For most celestial bodies, there's no difference. You tell it to go into orbit, and it just stops there. The icon on the sidebar will be red, showing it as idle.

For some bodies, specifically planets that you own, it will put the ship in orbit, which is different than simply being nearby. The icon on the sidebar will be green, indicating orbit.

When in orbit around one of your planets, fleets:

• have reduced upkeep costs
• can be repaired
• can be upgraded
• can be affected by spaceport modules, such as the Crew Quarters which reduces upkeep costs
• will merge with any new ships constructed at the planet

Fleets also need to be in orbit in order to bombard a planet, and transport fleets must be in orbit in order to land their troops.