I have run into the same issue and haven't seen any solutions. The work around would be to create a custom action just for Salesforce1, perhaps replicating the action of the button with JavaScript that redirects the user to the Visualforce page.
I've just submitted an idea to Salesforce for this fix if you'd like to vote for it:
https://success.salesforce.com/ideaView?id=08730000000DoTIAA0
Until then I'll likely need to replicate buttons with actions. With Summer '15, it looks like there's a new option on the page layout that allows you to override which actions/buttons are shown on Salesforce1 vs the desktop so we won't have to have duplicates.