Is there any way to prevent sectors from building on a specific tile of a planet?

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.