There is no way to qualify a lead without automatically creating an opportunity. This is a new "feature" in CRM 2013. Hopefully it is one that Microsoft will provide a fix for. Here are several options that you can consider.
(1) USER RE-TRAINING TO DISQUALIFY
If you're using the guided processes in CRM 2013, your users can create an Account/Contact from the guided process. If it doesn't exist, they just choose "+ NEW" from the bottom of the drop-down. This is a new feature that is really helpful.
* If an account and/or contact already exist, you can just point to those
* If one or both don't already exist, then you can create them without leaving the lead form - and information maps over to the new record just as if you had converted the lead
Next, if there is not yet an opportunity, then train your users to DISQUALIFY the lead (you may want to add a new status reason such as "converted" for this purpose; I believe you could also set the workflow to set the status back to "qualified" based on the value of the "create opportunity" field if you wanted to).
Using this approach, you've accomplished the same thing as converting a lead without creating an opportunity. It's about the same number of steps too - but it gives your users a few more options in the process.
(2) USE A WORKFLOW TO DELETE THE OPPORTUNITY (UNTESTED)
You could also put a checkbox on the Lead form or guided process called something like "do not create opportunity". You could then create workflow on the opportunity entity OnCreate that checks to see if the Opportunity maps to a lead with this field selected and, if so, automatically delete the opportunity.
Warning: If using the included guided processes, the user will automatically be dropped onto the Opportunity form after the conversion. To avoid confusion, you should modify the guided process.
(3) RE-TRAIN USERS TO DELETE THE OPP
Someone else suggested this approach and this would work as well (though it would feel like an annoying additional step to your users).
(4) REPLACE THE CONVERSION PROCESS WITH A DIALOG
You can use a dialog to replace the existing conversion process. We had done this for several clients in CRM 2011. To make this seamless to your users, you'll need to update the ribbon menu to drop the existing qualify/disqualify buttons (on the form and on the grid views) and replace them with your own button that links to a dialog (otherwise you'll have to train them to go to the "..." and then choose "run dialog").
Your dialog would manually map the fields (so, if you add fields to the lead, account, contact and/or opportunity that need to be mapped, you'll have to update the dialog to update the mappings).
This is probably the most elegant solution (short of writing .NET code to use a pop-up form that contains everything you want).
(5) BRING BACK THE 2011 DIALOG (UNTESTED/UNSUPPORTED)
Microsoft may have left the old conversion dialog in place in 2013. If that's true, then you could use JavaScript (coupled with a new button on the ribbon menu) to bring that form up and, in theory, convert the record just as you always did.
I've not done the research to see if this method is still available.
Even if it is, there is a possibility that it still calls the newer function that creates an opportunity regardless of the user's selection. Or, if it doesn't do that, there is also a good chance that it will be eliminated in a future version of CRM and your code will break. So use this one at your own risk.
If you want to do a bit of research on this one yourself, you can load up a copy of CRM 2011 (assuming you are on prem and you have the ability to bring back past versions) and inspect the code behind the qualify button on the lead form - it will probably contain a call to the javascript function.
Hopefully one of the above options will provide a suitable workaround for you and your users.
