If you have the time, do it in two sections. I think it will be a more enjoyable hike and you won't have to pick alternate routes that are less than ideal. Fires, early snow, floods and even govt closures seem to put a crimp in a thru-hike plan.
If you only have one shot, do a thru ..but realize you may have to make some compromises due to the above. Some people are lucky and "thread the needle" and have no issues. But, well..they are lucky.
Just my opinion, Either way I am sure the CDT will be an awesome experience!