My initial reaction would be: Why do this? What is your motivation? Simply avoiding SQL in loops, or do you have some sort of operational problems you want to avoid?
Your exact query would not be that easy to convert into a single query because you do have tuples of ID and Order values that have to match in order to be deleted. Also notice that prepared statements usually do not accept an arbitrary number of parameters, so even if you'd be able to transform your query into the form DELETE FROM table WHERE (ID=1 AND Order=1000) OR (ID=4 AND Order=1234)..., you'd have to somehow work out how to fill the first, second, third ... placeholder. Additionally, you'd be forced to generate that prepared statement dynamically, which is probably the opposite of how prepared statements should be done when it comes to security.
If you have performance problems because deleting 1000 entries one after the other has a big impact, there are alternatives: If you wrap the deletion inside one single transaction, then it probably doesn't matter that much how many entries you delete - ALL of them will be deleted once the transaction is committed. Also note that using prepared statements is one way to speed up database operations - but only if you prepare them only once before you loop, and inside the loop you'd only pass new parameters again and again.
So to wrap it up: Undoing SQL in loops is not the best thing if the programming problem you want to solve is better solved using a loop, and there is no other problem related to it. If however there is such a problem, it has to be analyzed and mentioned - removing the loops isn't an automatic success story.