Currently users can't remove CIs from models, only add them. Given they can take hours to compute, this can be a hassle.
One way would be to make things like this work:
model$intervals = NULL model$intervals = model$intervals[-3]
An aid to learning would be to add a note to the help about remove = TRUE parameter to mxModel(), which would remove a CI of that name from the model.
newModel = mxModel(oldModel, mxCI("a_r1_c1"), remove = TRUE)