I would think that your proposal would damage the appearance of the matte finish on the metal and leave a much larger,even more annoying area of damage.
I agree.. I use t-cut occasionally for cutting paintwork, but you need to be careful with it, as any more than a little rubbing will definately cause the area to become shiny, and likely stand out even more. For high glossy surfaces it's great, but not much good for mat finishes, as it will definately change the colour of the area where your've been rubbing, probably make it look glossy.
TBH, I think I would just leave it as is, as you will likely make it look worse... I would put a decent cover on it.
My iPad slides into a soft leather folio case, but I always check in case there's any bits or something stuck to the case which might scratch it when sliding it in, I use a bits of sellotape to lift any bits off, as it does look like the rear of the iPad would scratch quite easily, and all it would take is a tiny bit of grit.
My advice to people is to carefully insert the connector BEFORE you plug it into the power adapter, your'll find it much easier to line it up and less likely to slip and scratch down the side, which is dead easy to happen on the iPad2 & 3. I was almost tempted to stick a piece of plastic protective around the connector, but was unsure how the adhesive may react with the iPads finish... I recall doing something similar with another device years ago to protect something and when I peeled it off months later it had somehow left a rectangular mark on the matt finish, so one has to be careful what you use.. on that occasion it was just a strip of plain clear selotape, but you could see where it had been. :-(