I'm very glad BioWare went this route with Bull. This is real consequence, unlike the other major decisions of the game you're not always going to get the most desirable outcome based upon your choices.
Dragon Age and Mass Effect have both missed the mark when it comes to "choices with real consequence." And while Bull's betrayal certainly isn't as fleshed out and well done as it could've been, it was definitely a step in the right direction imo.
There is no "correct" choice to make. Bull staying loyal to you does not imply you made a "correct" choice, nor does him betraying you imply that you made the "wrong" choice. It's not black and white.
If you encourage the alliance, Bull is cruelly reminded of who he is, what his true intentions are, and what he stands for. He is acting accordingly and I'm glad BioWare hasn't compromised his character in doing this. This is excellent character development and evolution.
While I have my issues with Bull as a companion myself, I really do respect his personal battle with his identity, and I'm glad that the direction we steer actually does make a difference in his life, as well as our own (speaking of our Inquisitors).
Btw, to anyone who sacrificed the Chargers just to get that Archon Staff schematic, that is extremely petty. Practical, but petty. It's disrespectful to the decision itself.
One final point: if I continue to do playthroughs in the future, I won't let this foreseen knowledge of Bull's betrayal influence my decision in the slightest regarding his personal quest. Decisions should be made organically by the player and in alignment with the morals/philosophy of your Inquisitor.