When the lifeform is transported off of Lt. Torres, there are no entry wounds or tears in her uniform from where it had attached itself to her internal organs.
The Doctor and Crell are transferred from Holodeck two over to the sickbay. Since they are both holograms, this is something that can easily be done. The Doctor, however, has his mobile emitter on at the time. This is a physical piece of equipment, but it is shown to transfer over as though it was holographic.
However, this could have been accomplished by a synchronized side-to-side beam transfer.
If the presence of Dr. Moset's image is so offensive to Lt. Torres, there are several options which the characters could take: Transfer Moset's knowledge to the regular Doctor's data banks, so that only Lewis Zimmerman's hologram need be seen in the operating room; or, with a single computer command, alter Moset's appearance so that he doesn't look Cardassian. If you think of it, you can imagine several more obvious common sense scenarios along these lines; however, their real moral qualm is using the research of someone who created that research in heinous ways. Changing his appearance or moving the information around doesn't change where it came from.
A major plot line in the story is how Star Fleet crewmembers react with racism to the Cardassian holo-doctor; therefore it is incorrect to reimagine the crew simply changing the appearance of the Cardassian.
After Voyager had been contacted for help by the wave, Tuvok said there was minor damage done... however when Janeway is trying to make sense of the events that just took place. She stated "It's strange, the wave followed us, didn't cause any damage...". This is clearly not correct because Tuvok just said there was minor damage done to the ship.
Harry Kim seemed to have created the Dr. Crell Moset hologram fairly quickly, yet when the ethical issue arises the crew never considers having the Doctor choose the next best exobiologist from the database and create a new hologram.