Full disclaimer, this is a destructive operation in some cases, and I mostly use it to remigrate parts of the system without affecting the DB. 
Have you tried doing it via the table django_migrations? Just remove the rows that map to the app label and the migration names in question and delete those rows.
+----+-----------------------+----------------------------------------------------------+---------------------+
| id | app                   | name                                                     | applied             |
+----+-----------------------+----------------------------------------------------------+---------------------+
|  1 | contenttypes          | 0001_initial                                             | 2015-03-07 16:32    |
| 30 | homepage              | 0001_initial                                             | 2015-04-02 13:30:44 |
| 31 | homepage              | 0002_auto_20150408_1751                                  | 2015-04-08 12:24:55 |
| 32 | homepage              | 0003_remove_mappinghomepagemoduleinventory_inventoryinfo | 2015-04-09 08:09:59 |
+----+-----------------------+----------------------------------------------------------+---------------------+
So now if i want to remove homepage, I can just delete row 30, 31, 32.
Of course since you dropped the tables too, you'd need to change django_content_type too:
+----+----------------------------------------+-----------------------+--------------------------------------+
| id | name                                   | app_label             | model                                |
+----+----------------------------------------+-----------------------+--------------------------------------+
|  1 | content type                           | contenttypes          | contenttype                          |
|  2 | session                                | sessions              | session                              |
|  3 | site                                   | sites                 | site                                 |
| 92 | master_homepagemodule_extrafields      | homepage              | masterhomepagemoduleextrafields      |
| 93 | mapping_homepagemodule_inventory       | homepage              | mappinghomepagemoduleinventory       |
| 94 | master_homepagemodule_inventoryfields  | homepage              | masterhomepagemoduleinventoryfields  |
| 95 | mapping_homepagemodule_inventoryfields | homepage              | mappinghomepagemoduleinventoryfields |
| 96 | master_homepagemodule                  | homepage              | masterhomepagemodule                 |
| 97 | mapping_homepagemodule_extrafields     | homepage              | mappinghomepagemoduleextrafields     |
+----+----------------------------------------+-----------------------+--------------------------------------+
So now you'd have to remove the tables that you need to remigrate need by dropping the rows for those tables.
I've used this when time was scarce and we needed a quick dirty fix, or when playing around in development.
Hope it helps you too!