Conversation threading is a core function of the Google Apps mail service. The natural grouping of a conversation thread between recipients help to keep context within the thread.
In the case of wanting to delete one, rather than all of the emails, in a thread, simply click on the link in the email controls for “Delete this message”
The individual message will be deleted from the thread.
New Options Arrived
Conversation threading can be toggled to “Off” within Google Apps. You can find this in the mail Settings>General Settings>Conversation View area.
When turning off the default conversation view, emails will be itemized individually within your inbox rather than grouped by conversations.