The title asks if punishing apostasy is evil. The opening post asks if it's immoral.
I consider "evil" and "immoral" to be very different in meaning.
To me it really depends on the form and extent of what you're calling punishment. If you're talking about physical punishment, or anything designed to take down/destroy a person for leaving, I think that's wrong.
I think it's wrong to take any sort of negative action against a person for simply choosing to leave, anything even close to coming from a place the other person does not have right to leave.
I think a group has a right to defend itself, so if the person is trying to come into the church buildings, and present a problem, or if the person is talking/writing/accusing the church and it's members of terrible things, the church has the right to defend itself, and for those church members to choose not to talk to that person -- just like if a person has a friend (or an ex) that is going around badmouthing them, I think it's ok to refuse to be in that person's company -- and to refuse to communicate with the person.