The real answer? You need group theory coupled with spectroscopic data to get an accurate MO diagram. The MO diagrams that you study in beginning chemistry are Disneyland. They let you practice and learn the same concepts that you can apply to real MO diagrams, but the diagrams you are studying are idealized (i.e.not real). They avoid the complications of the orbitals shifting positions which happens all the time. Using such diagrams, you would get a BO of 2.5 because the real order of the orbitals in CO had been neglected.
You should just be aware that the order of the orbitals need not follow that simple order of filling that it does. In fact, there are variations in the order of filling even amongst simple molecules. For instance, the MO diagrams for the valence levels of Li
2, B
2, C
2, and N
2 are filled so that the 2p-pi orbitals fill before the single 2p-sigma orbital. It is only for O
2 and F
2 that the 2p-sigma orbitals come before the 2p-pi orbitals when you are filling. Since in this case the inversion doesn't involve antibonding orbitals you can ignore the actual filling order of the orbitals and still get correct bond orders (however, notice how in the CO configuration I wrote I was careful to place the 2p-pi orbitals before the 2p-sigma orbitals following the pattern in the order of filling set by C
2).
Sadly, it will be quite some time before you can get into Group Theory. It is normally introduced much later in your education (Inorganic Chemistry was my first exposure), and if you are a biology major you will likely never have to experience it