Can't delete Relation module
One thing to check is if there are still fields using this field? Take a look at admin/reports/fields to see if there is anything using the relation fields.

Once you are certain...

If you are certain that there are no dependencies relying on this module, then you can open phpmyadmin, and look at the system table.

Look for /sites/all/modules/relation.info and change the status from "1" to "0". Do the same for relation endpoints as well.

This will disable the module manually.

I would recommend doing a good backup, or even better, recreate your environment away from your production site and test there.