your best bet might be to install civicrm in the "default" place and then move it over to the aegir branch and fix the settings file
you might also want to check:
http://civicrm.org/blogs/scyrma/civicrm-and-aegirand check with koumbit on the current status. I also know davej from circle has been installing civi via aegir recently so they might be of more help
lobo