Recently, I was doing the suicide mission and chose a romanced Jack for squad leader to experience Bobby's audio file in game, and yeah I regret it. Jack's line about dying when she's finally happy, actually didn't resonate with me that much, it happens so quick. Jack's dialogue in game while in the squad leader role, is what's painful to hear, as basically your listening to her die. The coffin scene at the end of the game never really effected me on any meaningful level emotionally until this, when it's Jack and Shep loves her. I realized that Jack is now my Murtock, and found myself thinking about Jack's line, "death is a ****ing on/off switch," and how the pain of Murtock's death burrowing under the skin. In my mind Jack got a proper funeral, since Garrus realizing what she meant to me carried her back to the ship(since its the kind of guy he is), she may not have cared but I did.
It got me thinking about the suicide mission as a whole, with a the negativity surrounding it, in the sense that a large number of people don't like it because its too easy, the finally boss sucks etc. After Virmire most of us wanted the opportunity, to save everyone in any future situation, and they gave us want we wanted. Basically, what I wanted to say on this is that if you want the suicide mission to be an emotional engaging experience the onus is on the player. From a role playing perspective it does seem pretty far fetched that Shep would allow his feelings of Jack to cloud is judgment, since Jack is clearly not suited for the role, but not completely out of the realm of possibility.