Theres no intelligent way of doing that except to rotate the object back and counter rotate it to position. NOW this WILL accululate numerical inprecicion over time.
Offcourse you can allways use a series of history to make the user THINK the scale manip is skewed (this woudl essentiay be mel to amke a atool that has arbitrary scaleing)
Not its rether easy to remake the scele tool in maya api to be eble to scale in any space tough.
However what i do suggest is to freeze ON export only and then whan the export is doen delete the freeze node. to be back where you started form. Wich essentoialy means make your pipe smarter.