The vanilla Revit MAJ export does not give you the option to turn holes off, but there is a switch in the API. You need an addin to access it. I will release mine some time in the near future.
If your straight ITM has Option 'Machine Cut If Dynamic Branches' set to 'Yes' and has taps connected in Revit, it will export with holes and Cut Type: Machine Cut.
To prevent in the future, edit the item in your database to set that option to 'No'. To deal with your current model or if you need that to remain 'Yes', run a script that sets it to 'No' and then wipe the holes.
Execute this script:
select item.cid
case 866
item.option[Machine Cut If Dynamic Branches].value = "No"
end select
item.update()Then mapfilter CID 866 and run command 'UPDATEDYNAMICHOLES'
Edit: whoops, I thought this was in the CADmep Users forum, not CAM. I guess you are asking if you can execute a command within a script. I'm not aware of a way to do that. See here:
http://www.xtracad.com/forum/index.php/topic,16090.msg106986.html