It doesn't sound like a very dignified experience at all and does highlight an issue within the aviation sector of accessibilty. A lot of the current aircraft interiors were designed many years ago, Boeing 737s (such as those used by bmibaby) were designed (and in some case built) in the era of Pacers and high step entrance buses. There aren't many disabled facilities on a Pacer, likewise an aircraft interior. Looking 20 years ahead though, I think disabled loos and accessible seating will come. It isn't that long ago when a disabled passenger couldn't use any standard buses in the UK.
However, I took my grandma last year to Germany, who is also wheelchair bound and the experience was fine actually. The transfer chair process was undertaken before security in a quiet area on both legs of the journey. Mind you, I have to be honest with you, she's firmly older generation and thought it was wonderful that a "nice chatty guy" helped her about.
The terminal staff aren't employed by bmibaby, the vast majority are instead employed by a contractor (that sometimes even includes staff in an airline's uniform). There is also a contractor handling special assistance and I believe they set the policies for the transfer of disabled passengers to the aircraft. This isn't airline specific and the staff there are fundamentally unskilled workers.
Being made to sit at a window is not something I've heard of before, I'd have thought the aisle would have made more sense!