I think I found another workaround to Matthew's, that should be easier to maintain over time:
1. Publish the the service with all fields displayed.
2. In Portal, open the visualization tab for the published item.
3. Make desited changes to the layer's pop up configuration.
4. And here's the trick - saves as new layer - which basically creates another item - referencing the same data. This is important because if you just save the changes to the first item - these changes would get overriden the next time you overwrite your service.