First of all, congratulations on the publication. The first is especially exciting, and I'm sorry the editing has marred your experience. Usually the keen eye of an editor has a positive impact, and I hope you can go into the next publication not stinging too badly from this one.
Many editors will run edits by an author, sometimes in the form of what's called a galley proof. This is essentially a document that shows how the text will appear in the publication, formatting and all. A good writer will be open to these changes. Editors, after all, are working toward the same aim you are: presenting the best work possible. Getting author approval on edits is common with literary journals and book publications, but less so with magazines and newspapers. Each publication has its own process. In the future, you can ask to see any edits before publication, and some publications may grant this.
While that's all good to keep in mind for the next publication, what do you do with this one? If the changes aren't egregiously wrong, let the work stand on its own. You'll look like an amateur pointing them out after it has been published. If they are egregious, then you might mention that when using that work as a sample. You can avoid the situation entirely, though, by sending your version of the essay when called to provide writing samples. While it's common to send a clip right out of the publication for magazine and newspaper articles, you can certainly send your own manuscript for samples from books and anthologies. And don't make an issue out of why you're choosing to go that route. Snipping about past editors can make you seem like a writer who's difficult to work with, even if your concerns are valid.