GAT,
I can tell you what I think would be a good practice but cannot assure you that this is common or accepted practice.
I would fit the structural model both ways and compare with a chi-square difference test. You can also compare the fit of each structural model to the corresponding CFA (with or without equality constraints). If the structural model with equality constraints fits as well as the models in which it is nested, then that bodes well. You can then do the rest of the things that you would ordinarily do to critically evaluate the constrained structural model solution. If the constrained model does not fit, then at least you have an a priori test of the more general model before you switch from confirmatory to exploratory mode.
If the structural model is well specified, it should reproduce the same covariance structure among the latent variables that you saw in the CFA. As a result, you should expect the parameter estimates for the parameters in the measurement part of the full structural model to closely reproduce the estimates that you obtained in the CFA. If not, that could be a sign if mis-specification in the structural portion of the model.
Keith
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Keith A. Markus
John Jay College of Criminal Justice, CUNY
http://jjcweb.jjay.cuny.edu/kmarkusFrontiers of Test Validity Theory: Measurement, Causation and Meaning.
http://www.routledge.com/books/details/9781841692203/