I don’t know what the situation was back when the project started, but if you now look at the DITA-OT Java package org.dita.dost, it makes you think why didn’t they choose something else. The package org.dita looks correct, but if you visit dita.org you’ll see that the domain is used to host a personal website.
There is no real reason to change the current package name, but you have to admit that e.g. net.sf.dita-ot or org.xml.dita would have been more suitable.