First let me offer the preface: I have ME on steam, but ME2 on PS3. This means my save file won't carry, so excuse me if this problem is addressed by that wonderful feature.

So, in preparation for Mass Effect 3 (as I'm the kind of terrible person who'll wait 'til I can buy it with the DLC, so I have plenty of time), I've started the first one again. Booting up the character creator I carved myself a Sole Survivor, a back story which I'd found intriguing in ME2 but had yet to try in the original. To my delight the first game is much better at bringing this up at every occasion possible. Linking side-quests and dialogue options in seamlessly. Well, actually that's a lie. It makes it glaringly obvious that it's pandering to your particular story, but it's nice that they're acknowledging it nonetheless.

ANYWAY, I'm off on the Sole Survivor specific sidquest (Newton system), and I run into my old buddy Toombs. He's a pretty simple guy really, but he has a lot to say about Cerberus. Namely that they caused what is probably the most traumatic event OF YOUR LIFE. THE EVENT WHICH YOU NOW INESCAPABLY BLAME YOURSELF FOR EVERY DAY. THEY MURDERED YOUR FRIENDS.

Now I know through repeated trial that all dialogue options in the second game lead to "Well, I guess I'll have to join Cerberus then." However, those of you with saves, does Shepard acknowledge at all that his new employers are basically the people he's (presumably) been trying to track down and destroy throughout this process of saving the galaxy? It just seems slightly odd that he's so at ease with the situation, given how much he should (theoretically) hate their guts.

I'm playing through as a Sole Survivor right now and up until now (and as far back as I remember)... nope. Besides the "Well, Cerberus time, I guess" that you mentioned, I don't remember much Cerb hate.
 
Though:

No, it's not really an issue. ME2 is not very confrontational in that respect. Others may correct me if I'm wrong on this or maybe I just haven't experienced those possibilties. Right at the beginning of ME2 Sheppard has the dialogue option of remembering the name Cerberus, but I think that's more or less it.

Be that as it may, I've always played ME2 like Sheppard is effectively just using Cerberus as a means to an end. Pretty much always going renegade option when talking to the Illusive Man. If they want to give me money and equipment for my own goals then so be it. They are not my friends, but my enemy's enemy.

Sheppard's backstory is not really an issue in ME2 in general and apart from a few moments in ME1 as well. Dialogue changes a little bit and some encounters as well, but on the whole that's about it as I recall. But then again it has been a while...

The enemy of my enemy is my friend.

Sole Survivor Shephard really doesn't like working with the fuckers that did that, but he does realize that they have the money, the resources, and the will to take on a threat that those useless council assholes won't do anything about. They're a means to an end, and both sides receive a benefit from the others' work regardless of hate. Not working with Cerberus for the events of ME2 would have been boneheaded and would have gotten in the way of saving millions of lives. Personal vendettas had to wait for the good of others.

the lair of the shadow broker dlc mentions it.