It is not the simple way to update by magento connect. I most of the time get problems with apache as it is most of the time too long to run. The best is to copy the new sources on your installation and open the website (best to call index.php from cli).
The website and the database will be automatically upgraded.
The reasons that can push you not to do so :
- your installation contains overwrite of core sources in the core itself (really bad practice). The update throught connect would not be better indeed...
- you changed basic magento files in the default theme (bad practice as well). The update will destroy your templates...
- you modified basic magento files in the lib, shell or skin folders (still bad practice)
If not, then go on... Think to put website in maintenance before running and flush cache and recompile after it.