At the moment, there is not much space in INFILTRATION when it comes to players' decision. Five rooms - roll twice in each one of them. Defcon goes down and it can go up.
If those rooms are arranged in a strict sequence (1st-2nd-3rd-4th-5th), how about adding a choice of passages between them: more ordinary option (corridor, a modifier /harder/ to clear next room but also a benefit, maybe a bonus to search) and more clandestine option (air ducts? easier to clear the next room). There must be some risk/reward in such a choice. Those choices do not have to repeat/ be the same before each room.
This can be connected with giving some flavor/ modifiers to the rooms when it comes to Clearing and Search rolls - 1st room could be a "guarded entrance"/main gate - difficult to clear, very little to find/search for but maybe our intrepid spy will find a sewer entrance that will allow him to bypass the guard. Eventually, one can infiltrate an employee break room (?), where clearing and search is easier than anywhere else (provided no one is taking their break :) ).
Another possible space for giving a choice to the player would be allowing to select a sequence of clearing the rooms (especially if there are 'easier rooms' and 'difficult rooms').