no, i think he knew he was attracted to her before butterflied. and that he was very much conscious of this. it wasnt a sudden decision he made right there, about not being able to do it-so i think he'd been thinking about it, and had been aware of it for a while.
i think by season 4, he was clearly attracted to her, in awe of her, he knew he could care (although i think personally he already did care about her on a personal level by butterflied, he just couldnt say it out loud, probably in denial-not deeply, but there were feelings there). but i think he was also super concious that it was a disaster situation for him professionally that he was interested in her, and i think, like he did in season 3 when he realised he might be getting too close, he kinda pushed her away a bit or pretended to himself he didnt so he'd feel better, but i do think he was concious of the repercussions if he led her on, and anything happened, so he kinda backed off, thinking there was no way this could ever end happily. so maybe he actually started believing it, like in invisible evidence, he looked shocked and like eh wtf?...as he did in snakes...shocked. i think maybe he convinced himself she would get over him, and everything could go back to how it was, but despite that, he was happy to get close to her under the cover of professionalism. ie: invisible evidence.
but PLEASE. that invisible evidence scene, is blatently sexually charged, and grissom himself creates it, the way he talks to her, c'mon, its slow and flirty and sexy, especially the 'like this' line. and the way he moves his hands to her waist....thats supposed to be her superviser!, it seemed inappropriate from that standpoint because there was tension there, before he even did that, and he didnt back off, it was sara who did. he was totally aware of his attraction to her.
but because of the writers not always been too sure of the pairing, its hard to establish a timeline, as to when his feelings grew or when he actually realised it.
i do think though, though he was concious of his feelings towards her, he was probably in denial at certian points, but that, he did know how he felt.
but maybe in Butterflied he realised just how much, he could/did care. because when faced with the prospect of the Victim that resembled sara, he became obsessed with the case, and couldnt look at, or speak to sara. and he made sure she did the perimiter, totally away from him, distancing himself from her. i think maybe its possible that the reality of a girl dead, that looked like sara, and the way he acted on that case, made him realise how he felt about sara, hence his reflection at the end of the ep. but he knew he was attracted to her prior to that, IE showed that in my opinion.