The ODT 11.2 Beta 2 is only designed to work with the ODP.NET 11.2 Beta 2. It probably will work with ODP.NET 12c (though we haven't tested it), but I don't see why you need to unconfigure it even if you install ODP.NET 12c.
Have the ODT beta continue to use the ODP.NET beta. Then just use ODP.NET 12c to develop your applications.
If you can wait a week or so, we'll have an ODAC 12c download available so that you don't need to perform two installs and can use production software.
If you do install managed ODP.NET from the Oracle DB 12c client, there is an additional configuration script to manually run. This only applies to managed ODP.NET in the DB 12c install. It doesn't apply to any ODAC install.