HI Alex, there is an option in MoI that you can use for that currently. In MoI go to Options > Import/Export > FBX options and set the option for "FBX version" to something later than 2010/6.1 .
If you want you can set Apply Transformations in the import dialog. This will set the scale to zero and make the model, well correctly transformed.
I had been using OBJ but after Micheal's comment I thought I would give FBX another go, it works perfectly.