How to stop maps, photos, and ibooks from loading in dock on startup
This should solve your problem: https://jamfnation.jamfsoftware.com/discussion.html?id=12266

You have to edit the following file: /System/Library/CoreServices/Dock.app/Contents/Resources/com.apple.dockfixup.plist

Right below &lt;key&gt;add-app&lt;/key&gt;, you can remove all the &lt;dict&gt;...&lt;/dict&gt; related to the apps you don't want to appear in the Dock on startup.

[EDIT]
It looks like this file cannot be edited anymore with El Capitan due to the System Integrity Protection (SIP). See this discussion about it.