You could contact someone from the Apps/Partners team to see if they could remove the listing for you.
I'm not entirely sure if there is a way for an app developer to unlist an application.
If you wanted, what you could do is add some of your own listing logic internally that lets you reject new signups by giving the user a "Sorry signups are closed for the time being" page. That UX is kinda ghetto though since that would be equivalent to having an app in the App Store or Play Store and having it tell you that you aren't allowed to use it yet.
Though... it worked for Mailbox so you never know :)
We'd be happy to get your application unlisted for you; if you just fire off an email to firstname.lastname@example.org, myself or someone on the team will get in taken down for you.
You can find the steps here: https://help.shopify.com/en/manual/apps/working-with-apps#uninstall-an-app