I've only played Siege of Dragonspear twice. The first time I didn't have Imoen in my party at the end of BG1, so that's that.
However this time I did
and when I started SOD Imoen wasn't replaced by Safana. I was just a member down (had 5 members for the initial dungeon.)
Was this a change? All I've ever read on these forums is that if you have Imoen, she's replaced by Safana.