The Content with Style blog has this quick tip on removing nodes from inside of a SimpleXML object without causing problems with its internal handling.

You might think otherwise and hack it with unset(), as it was done in one of the web applications I inherited at work, but today I found out that this works under some conditions, but not with every setup. I'd love to tell you what exactly the differences are that make it break, but I didn't spend the time tracking it down.

Instead, he suggests a call to dom_import_simplexml to swap the object over to the DOM, performing a removeChild on the node and pushing it back over to SimpleXML if the need's there.