Speaking of having only one doctor... thats another reason he shouldn't have "killed" the Equinox EMH, just disabled him and reinstated his ethical sub routines.
Where's the hue and cry over him killing his "brother",
a "being" that was mentally savaged by his crew (as much as "our EMH was savaged by Ransom) that Janeway has to deal with over Tuvix?
I would imagine that there was only one EMH because you hope to never have to use even the one. He was designed to be used in an emergency only and for a short time. Even still his program was very large and it might be that having two of them would take up too much space
You'd think that the sort of emergency that would kill the real doctor would necessitate multiple EMHs. You wouldn't need multiple copies of the EMH program on the computer anyway, just one program projecting multiple doctors. Maybe even give the Doc the ability to fragment into two or three and then reintegrate himself back to one when the emergency is over.
It seems the writers wanted to make the EMH as human as possible to make him relatable to the audience, and in doing so removed most of the benefits of having a holographic doctor.