I sent this question to support and here's their response:
In order to deploy a Manipulate dynamic object without the originating cell, we can use the function CDFDeploy. CDFDeploy will create a CDF file on the desired location based only on the expression given. Therefore, I suggest using the function to create such CDF file, for example:
d = Manipulate[Plot[Sin[x (1 + a x)], {x, 0, 6}], {a, 0, 2}];
CDFDeploy["manipulate.cdf", d]
The above will create a CDF file with the Manipulate created on the default Directory[]. You can also give a path to the resulting file.
