It's a matter of taste. I you don't like the look of it you can cut it off. Elderberries can take a lot of cutting. But that branch is the one which will flower this spring, if any of them do on such a young plant. The new shoots from the base could be just as long by the end of the year so it won't look so odd.

BTW are you aware how big they grow? That pot will not last it more than a year or so.

stake the branch up. It will be fine.