Ovious this response too late for OP, but because I trawled this up as others will likely do in future:
This is to do with Maya's AttributeEditor tempalte handling of multi's. It is recreating (some) of your multis post-deletion.
If you dont let the AEd see your node (or, dont expose your multi attributes [presumably]), then you wont have a poblem. There are solutions to preventing this behaviour of the AEd, but they are a touch intefere-y with the base, so i wont post.
Handling of multis and undo/redo is another matter altogether, and is going to proove a headache as we go into supporting undo across the board for large rig setups. I think 2015 api added support for deletion of multis, so this may well harbour for greater undo support on multis, yet to see.