From what I've heard, yes it would often be harder to build a commercial building instead of a residential one. With the permitting process for commercial buildings, you may be expected to follow certain codes and compliance requirements in your area. You may also need detailed plans on what you want to do, consultations from professionals, and you may even need to take it up in public hearings or to your city council for review.
You could open the business as quietly as you can, but that may be easier said than done. But it seems to be possible. I'd start by not revealing the details of your new business to the public, such as avoiding press releases and or doing public events. As well, make sure you focus on making this new business legal and fulfill only the legal requirements for public notice.
Another thing you can do, is to engage with your community and address any concerns the community members have in private. If they hear it from you, in person, it might go over better. If you're worried about doing this all on your own, you could reach out to experienced pros in the field to help walk you through the permitting process for this type of development.
Keep in mind though, that you won't be able to go through this process 100% quietly, the community and the city will eventually need to know what you have planned.
Here are some of the links I found that helped me answer this:
Differences between Residential and Commercial building permits
Residential vs Commercial Building Permits
How To Stop Telling People Your Business