I agree that the federal government can regulate who comes in and out of the country.
I like when you say "In order to remain in power, a government must resist those enemies that seek to undermine and destroy it" because it rightly draws no distinction between aliens and citizens. If a person is trying to bring down the government, the government can stop him or her, regardless of citizenship.
What I question is whether we want to live in a society where any advocacy of gun control is grounds for the government to go after someone. After all, if Pierce Morgan advocating gun control truly is an attempt to destroy the United States government, then it is equally true that any Joe Schmo American citizens doing the same is likewise conspiring against America and can be punished by the government. And then once this broad view becomes precedent, who knows what other types of speech would be considered seditious?
Let's leave deportation to people who have come to this country illegally, stayed beyond their legal time frame, who break other laws, or who are, in a very direct and provable way, trying to bring down the government (e.g., there is evidence of a plot to blow up a federal building).