Not really, but you can use UndoModes to collapse all changes into a single undo...
a little old topic but I actualy got the same question.
I am automating InDesign (CS5.5 - CC) using VB.NET compiled as exe.
the exe is started from SDK plug-in.
For this reason the UndoMode is not an option because I do not use DoScript.
Saving document while processing it to clear Undo is also too slow.
I am asking myself if it would be possible to create small scriptable plug-in which could be accessed from VB.NET to clear undo each time it is called?
thx in advance