In my opinion I would keep the cone on as much as you can.... I know it sucks, but he will get used to it - and will heal properly and in a timely fashion.
I also read that if you keep taking it off and on and off and on too much, the dog will almost think of it as a punishment.
When Banksy just had his eye infection I kept it on most of the time, however took it off occasionally if I knew he would not leave my sight. and it was kind of sad the look he would give me when I went to put it back on, like he did something wrong
There is an inflatable cone you can get that is more comfy - I did a post in the health forum called the cone of sadness and someone posted a photo of it - I plan on getting that one when Banksy gets neutered, which is soon.
It's so sad seeing them so down - Hope he feels better soon <3