At the time I did not know it, but ALL stored procedures were dropped from the database. ALL views were dropped from the database. Only table schema should have been altered in the DB, right? Did I blow by some checkbox somewhere that says, "Drop all SPs/Views"? What configuration of the DDT would cause this behavior?
This could be right depending on how you have deployed to this machine in the past. Any SPROC, view, UDF, etc. that was created outside of the DDT will be left alone...assuming that that sproc, view, or UDF has never been deployed by the DDT. When the DDT deploys a SPROC, view , or UDF, it applies an attribute (Extended Property) to the entity in question so that it knows that it was deployed by the DDT and can safely be removed. So these stored procedures, views, or UDFs had to have that extended property applied to it.
Now if you are running an older version of the DDT, then it will do exactly what you mentioned regardless of the attribute. But if you are running on the latest version of the DDT (1.6.6 or better) then this will not happen....and I am very confident that this works because I recently talked to someone who uses the DDT in an environment where there is a DB admin and the developers deploying to the same production server...and the scenario that you explained use to cause...well...let's just say, "some issues." 
But I recently asked them (with the last week) how this has been working for them and all is well. This is something that actually applied to our medical software as well...so I am confident that this is working as it should. But this should at least clue you in as to how the DDT treats these items.