Julia Galef watched a friend face this dilemma, and disapproved of her for throwing out the pepperoni. Considering that the order has been placed, and there was no undoing the damage, she thought that was irrational.
Here's what she doesn't get. If you haven't eaten meat for a long time, it can both taste good and seem unpleasant. Best guess: that's why the friend spurned the pepperoni.
But more interestingly, there's also this: When you choose a rule to follow, you have to consider the rule's content, but also the rule's followability. Giving up animal products is a discipline, for most people. It takes self-control. Take the rule "never eat pepperoni." That's a little overbroad, contentwise. It generates more abstinence than necessary, ethically speaking. Yet it's a great rule for many people, because it gets you out of the habit of eating pepperoni. It removes pepperoni-eating as an issue.
The alternative is "never eat pepperoni unless the meat would otherwise go to waste." It seems to make sense, but it isn't very followable. If you eat pepperoni on messed up orders, and off your friends' leftovers you'll be stimulating your yen for pepperoni. Adopting that rule is likely to generate less abstinence than necessary, ethically speaking. At least for pepperoni coveters, the simple rule is the way to go.
I would have thought this was obvious. In lots of areas of life, we follow over-broad rules. You follow a rule against stealing to keep you on course not to steal when it really counts. You follow a rule against lying because most of the time it's important not to lie. We wind up being more restrained than we really need to be, but it's for the best. (And we can still make exceptions, of course, when it's really important to do so.) Not eating pepperoni on that pizza is the same kind of thing. It keeps you on course to turn down pepperoni next time it actually matters.