Hi Owin,
The check-in actions per se are not a part of a work item type definition, however, there's a way to disable the "Resolve" option with a little bit of trickery. Open the Task work item's XML and locate the following lines:
Code Snippet
<ACTIONS>
<ACTION value="Microsoft.VSTS.Actions.Checkin"/>
</ACTIONS>
Now, remove these lines altogether (be sure to back up the XML before making any changes to it!) and upload the WI type definition back to the server. This should effectively disable the "Resolve" option. Unfortunately, there is no way to swap "Associate" and "Resolve".
P.S. I've checked this on my instance of TFS and Task.xml does have the quoted lines by default.