The big difference is that removal from the clerical state (which I think if the right term) is, for the most part, permanent. When someone is excommunicated, he/she just needs to reform, make a good confession and usually ask the Bishop to lift the excommunication. (there are a few that only the Pope can lift and some that pastors can lift) Once you are removed from the clerical state, you have no official position in the Church other than any lay person. When a priest is removed from the clerical state, the documents usually spell out what the priest can and cannot do. Sometimes, they are allowed to marry in the future, often they are not allowed to teach in a Catholic institution.
An excommunication is medicinal for something that has happened in the past. Removal from the clerical state is more about the future of the specific priest.
Oh and while excommunication is always a penalty, removal from the clerical state is sometimes done when there was no wrongdoing at all. It is not itself a penalty but may be the ultimate result of correction.