Just redid the convo with him a few times. He definately says he was chosen to execute the FM "Th-they picked me as the templar to strike the killing blow if... if you became an abomination."
Although, reading through this thread, I agree with Xandurpein in that it's more likely to be infatuation. One line makes me think he doesn't really know the FM very well -
FM: I knew I would not fail my Harrowing
Cullen: You've always been so confident... or so I hear.
If he doesn't know the FM very well, it's hardly likely he's in love with her. Could easily just have been that he had a small crush, one of the apprentices noticed it, told a few friends and the rumour grew until it was full-on love. Maybe he ran away because he didn't want the FM to think it was anything more than just a crush? Or maybe it was more and he's scared of his own feelings...
@ Addai67, I also don't find him creepy at all. I imagine he could be, and I think I see where others are coming from. Also, yeah, I did notice the Cullen/Alistair similarities. My current playthrough - female elf mage - is currently going out with Alistair because of that. She hasn't gone back to the Circle tower yet, maybe seeing Cullen there will influence her views on Templars and therefore on Ali too? (Gives me an excuse to ditch Ali and send her after Zevran

)
Also if you flirt with him and he runs off, does anyone know if you can find him in the Tower again before you leave to be recruited?
Truby-Liz