Hi Paul, welcome to the forum, I can totally relate to your feelings of guilt..
It's funny that you used food as an example, my family always have big roast dinners on New Year's Day, and today I cleared my plate except for two slices of meat.. Then felt really guilty about it and kept thinking about the poor turkey, starving children in the third world etc, this is the way I think all the time

You said in your post that you know in the grand scheme of things wasting some milk isn't worth feeling guilty over, so you've addressed your feelings of guilt and tried to work past them
I don't think there is a way to remove the guilty feelings completely, I believe guilt is a common part of depression
As long as you are able to notice that your feelings of guilt are excessive, hopefully that should help to ease it a little but short of drinking the dodgy milk there isn't a lot you can do sometimes :) I know how horrible guilt can be sometimes, especially when you start over thinking things, you're definitely not alone in the way you think
And I agree with Zaf about avoiding doing things again, it might even help you in the long run