Yes. There's a checkbox for each colony to turn off auto-upgrade. Disappointingly, it's always checked by default.
Personally, I tend to stagger upgrades. That is, I will happily run a tier 3 alongside a tier 2 or tier 1 building until I'm ready to upgrade them all to tier 4. If I'm desperately short on tiles and need to build something else I will demolish the lower tier building rather than using it in an upgrade, because the more times you upgrade a tile, the less benefit you get from doing so.
Also, I tend to do upgrades manually, when it is convenient for me. The only exception to this that I make are auto-terraforming projects, which are great as they always open up more tiles for use.