I've just realized why the crystal gems left Lapis trapped in the mirror.

Poofed gems are all unconscious. Not just the ones being held in bubbles, all of them. So the CGs assumed that Lapis, being poofed, was completely unconscious, with her energy just powering the mirror. That's why they were so surprised when they learned she could talk. They figured that keeping her in the mirror affected her no differently than keeping her in a bubble. Also, they probably assumed she had been corrupted the same as every other gem, and so letting her out would have just been more risk.