So I planned on stripping and overhauling the brakes. Whipped everything off and then realised I couldn't get the pistons out without reattaching the master cylinder, lever and hoses

So I did a bad thing - I used an adjustable wrench and a rag to pinch the tops of the pistons to gently lever them free

In doing so I marked each piston. I hate myself so much for being so ham fisted and lazy

They marks go no lower than 1-2 mm and will likely not even make it to the dust seals, but I did file down any roughness, using jeweler files. This of course removed a small amount of plating

My question is, do I need to worry about corrosion going under the existing plating and getting to the piston seals?

I am a naughty boy and I must be punished

naughty..naughty..lol..as long as they have been smoothed down and wont go to the fluid seals you will be ok,

hi, you can use a foot pump or even a bike pump to pop out your pistons but beware they fly out like a bullet. make sure the bleed screw is closed, wrap the caliper in a rag. put the end of the pump hose on the banjo bolt hole and give a short quick blast. if the pressure escapes put a rubber oil seal between the hose and bolt hole. as you know the area cleaned up will now be prone to rust and if you fit new pads the piston will be deeper into the dust and oil seal. on dual pistons you can chock them so both come out equally then reduce the thickness of the chock until they can be removed. again be careful.

Thanks. Very helpful