According to BSN (and quite a few YouTube videos - why yes, I do cheat a LOT), the guide is actually incorrect on that angle - he should still side with you as long as you're maxed out, did all the quests, got all the dialogues, etc. The whole thing is complete insanity, really. I didn't have any issues, but only because I metagame like a fiend - it's a little absurd that you have to break immersion and "cheat" to make sure all these little angles are covered.

And I agree on the Merrill angle - I wanted so much to like her, esp since I'm a huge fan of her VA, but that last quest especially... gah. This whole game is just, "Here, have some tragedy and stupidity and CONSTANT MISERY. Free box of tissues and stress-relief ball not included."

Glad I could be of help, anyway!