In that situation, you have several tools at your disposal. If you are friendly with the corp (they are in your alliance, or allied in some way), you can offer repayment or replacement of the object. You can promise punishment of the perpetrator. You can allow the other corp to seek out revenge on the perpetrator (although this can escalate quickly and be bad). You can say "Tough shit, be quiet or we boot you from the alliance".
If it happened to a neutral corp/alliance, you can use the weight of Goonfleet as leverage. Goonfleet is huge, with a lot of friends, so not many people want to start a war.
I didn't realize diplomats were in factions, I thought they were sort of independent, which is where my confusion arose. Thank you!