She has a captain level reiatsu. A dozen super powerful reiatsu fighting each other would probably crumple Inoue to the floor like it has in the past. Wheras Unohana with her reiatsu would be able to stay on her feet and move to where she is needed in healing.
I also think she has way more battlefield experience as a medic than Inoue, including situational awareness.
Obviously she isnt a fighter, have you seen her friggin Bankai lol
For the above reasons I think Shinji? made the comment(also because they possibly doubt her loyalties/reprogramming that may have been done to her subconscious), but IMO Inoue being there and being in trouble would be a driving factor for Ichigo to go apeshit mad on Aizen and transform into god mode, which I've always felt Bleach was leading up to. (Remember, ichigo keeps becoming stronger because he has to in order to protect his friends *cough Inoue*) Can he become stronger simply to kill Aizen if he isnt directly threatening anyone he really cares about?