It is possible that you are parsing the sentence as
What consideration do you make in leaving your desk?
This would be understandable because English often attaches prepositions to verbs to give idiomatic meanings, which cannot be discerned by considering the meanings of the verb and the preposition separately. The combination is a unit, which some call a phrasal verb. For instance, take make out, which has several different uses, one of which is to reach some result. Here's an example of the usage:
It's not clear how Johnson made out investing in real estate in the Sunshine State....
In other words, we're not sure of the result that Mr. Johnson achieved by putting his money in land investments in Florida, the so-called Sunshine State. Maybe he got rich; maybe he went broke. Notice that you can't figure out the meaning by putting together the definitions for made (fashioned) and out (outside).
Note also that this appears to have the same sequence as your example:
Form-of-to make + Preposition + Present-Participle
But make in is not a phrasal verb. The correct association is
What consideration do you make in leaving your desk?
The preposition is not part of the verb, but rather introduces the prepositional phrase with object leaving your desk.
Consideration here means careful thought, and it licenses a prepositional phrase with in or about to indicate the topic of that thought. Since the preposition is not closely associated with the verb, we may move the prepositional phrase to get the equivalent (though less elegant) sentence
What consideration in leaving your desk do you make?
Alas, there is no rule for figuring out which combinations make phrasal verbs.
