The CBA gives him the right to refuse.....conditioning is just the term for it in the CBA. It had nothing to do with his conditioning. In fact IIRC they gave him the option to do it because he hadn't been in the lineup for a longtime. It wasn't really a team request.
He may not be in future plans but it won't be because of that section of the CBA. It will be because of the waivers section IMO.
I think you are mistaken if you think his chances of being put in the lineup weren't reduced by a refusal.
He exercised his right not to shake tye rust off by playing a few games in the AHL. The Jets excercised their right to let him rot in the pressbox.