The living mind may be mistreated, grow sick, die a painful death. The uploaded mind may be mistreated, experience something equivalent.
Those sufferances are valid issues, but they are not arguments for the act of cloning itself to be considered a moral issue.
Uncontrolled diffusion of such uploads may be; I could certainly believe a future in which, say, every American politician gets a thousand copies of their mind stuck in a digital hell created by individual members the other party on computers in their basements that the party leaders never know about. But then, I have read Surface Detail by Iain M Banks.
The argument itself is symmetric, it applies just as well to your own continued existence as a human.
To deny that is to assert that consciousness is non-physical, i.e. a soul exists; the case in which a soul exists, brain uploads don't get them and don't get to be moral subjects.
Being on non-original hardware doesn't make a being inferior.
When the organ is question is the brain, that argument is correct.