While I typically do not favor making structural changes to a league after the season has started, this is one instance where I think it makes perfect sense to do it. The fact that some teams will not play each other during the season is reason enough to alter the schedule. Not having all teams face each other at least once does more to undermine the integrity and balance of the league than modifying the schedule. Additionally, the season is only in its 3rd week right now. Changing the schedule after this point will not have any detrimental effect on anyone.
I am also against going to the league members for a vote on this issue because there will unlikely be a consensus and having differing opinions will only complicate matters. This is an easy fix and should be handled directly by the Commissioner. If you make the decision and back it up with arguments such as the ones I gave, then your league members will have to accept it. It will make the situation less of a logistical and political nightmare for you.
If you don't have one already, I would recommend you draft a constitution for your league outlining all rules and guidelines, as well as providing a process for dealing with issues of first impression not delineated in the constitution. If you need any assistance or advice doing this, please feel free to contact me at firstname.lastname@example.org