It depends on what you have. If you have a batch that had some sulfur odors, leaving it on potentially stinky lees may be worse. If you are using yeast that can be funky (like 71B) then leaving it on the lees may be worse. If there is fruit pulp involved the lees may be worse.
On the other hand, if you have something with delicate fruit aroma, too much headspace may cause it to deteriorate. Obviously it acetic acid bacteria are present, or some lactic acid bacteria, too much headspace may lead to a spoiled batch
The fact is, both options can be bad. My answer is rack off the lees and take some action to prevent air in the headspace. See
this thread.