XML is in essence a file format. It is not generally used as an in memory representation of data from some other file format. Unless you want to store an intermediate form of the data on disk in some non-GEDCOM format XML is not appropriate. Even then, you would probably be better to store any intermediate form of the data on disk as a clean GEDCOM file (although, see below).

There are many ways to handle trees in Perl (see tree), but probably you are better to write a GEDCOM object hierarchy that directly addresses the structure you need to manipulate.

I note that GEDCOM 6.0 will be an XML based file, but that needn't alter how you internally represent the data. In fact whatever internal representation you choose now should be completely independent of the external representation and should be chosen to facilitate the creation and manipulation of the internal representation. Then it becomes fairly easy to handle different input file formats and generate different output file formats.